Starting phenix.real_space_refine on Sat Sep 12 11:11:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfx_13383/09_2026/7pfx_13383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfx_13383/09_2026/7pfx_13383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pfx_13383/09_2026/7pfx_13383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfx_13383/09_2026/7pfx_13383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pfx_13383/09_2026/7pfx_13383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfx_13383/09_2026/7pfx_13383.map" } resolution = 4.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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 354 5.49 5 S 10 5.16 5 C 7612 2.51 5 N 2606 2.21 5 O 3298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 13880 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "P" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "R" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3610 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "J" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3647 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "S" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 2.23, per 1000 atoms: 0.16 Number of scatterers: 13880 At special positions: 0 Unit cell: (149.1, 91.35, 122.85, 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 354 15.00 O 3298 8.00 N 2606 7.00 C 7612 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: 0.99 Conformation dependent library (CDL) restraints added in 276.9 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 69.4% alpha, 3.1% beta 177 base pairs and 311 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.593A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.521A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.039A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.346A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 37 through 49 Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 Processing helix chain 'N' and resid 104 through 123 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 77 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.583A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.088A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.652A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.207A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 89 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'Q' and resid 112 through 116 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 Processing helix chain 'R' and resid 103 through 124 Processing helix chain 'S' and resid 38 through 51 removed outlier: 4.088A pdb=" N LEU S 42 " --> pdb=" O PRO S 38 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER S 50 " --> pdb=" O ALA S 46 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS S 51 " --> pdb=" O VAL S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 69 Processing helix chain 'S' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.889A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.225A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.737A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.157A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'S' and resid 56 through 57 436 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 456 hydrogen bonds 912 hydrogen bond angles 0 basepair planarities 177 basepair parallelities 311 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2630 1.33 - 1.45: 5120 1.45 - 1.57: 6370 1.57 - 1.69: 706 1.69 - 1.82: 20 Bond restraints: 14846 Sorted by residual: bond pdb=" C3' DC I 455 " pdb=" O3' DC I 455 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C3' DC I 555 " pdb=" O3' DC I 555 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C3' DC I 554 " pdb=" C2' DC I 554 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C5' DA I 513 " pdb=" C4' DA I 513 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 1.01e+01 bond pdb=" C3' DG I 538 " pdb=" C2' DG I 538 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 21291 3.09 - 6.18: 244 6.18 - 9.27: 24 9.27 - 12.37: 3 12.37 - 15.46: 1 Bond angle restraints: 21563 Sorted by residual: angle pdb=" O4' DG I 544 " pdb=" C4' DG I 544 " pdb=" C3' DG I 544 " ideal model delta sigma weight residual 106.00 102.02 3.98 6.00e-01 2.78e+00 4.39e+01 angle pdb=" N GLU L 63 " pdb=" CA GLU L 63 " pdb=" CB GLU L 63 " ideal model delta sigma weight residual 110.28 118.62 -8.34 1.55e+00 4.16e-01 2.90e+01 angle pdb=" O4' DC I 524 " pdb=" C4' DC I 524 " pdb=" C3' DC I 524 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.90e+01 angle pdb=" O4' DG I 546 " pdb=" C4' DG I 546 " pdb=" C3' DG I 546 " ideal model delta sigma weight residual 106.00 102.78 3.22 6.00e-01 2.78e+00 2.87e+01 angle pdb=" O4' DA J 281 " pdb=" C4' DA J 281 " pdb=" C3' DA J 281 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 ... (remaining 21558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 6045 35.87 - 71.74: 1922 71.74 - 107.60: 34 107.60 - 143.47: 3 143.47 - 179.34: 3 Dihedral angle restraints: 8007 sinusoidal: 5576 harmonic: 2431 Sorted by residual: dihedral pdb=" CA ILE P 50 " pdb=" C ILE P 50 " pdb=" N TYR P 51 " pdb=" CA TYR P 51 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PRO R 103 " pdb=" C PRO R 103 " pdb=" N GLY R 104 " pdb=" CA GLY R 104 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE O 84 " pdb=" C PHE O 84 " pdb=" N GLN O 85 " pdb=" CA GLN O 85 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 8004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1777 0.051 - 0.102: 552 0.102 - 0.153: 107 0.153 - 0.205: 16 0.205 - 0.256: 4 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CG LEU Q 23 " pdb=" CB LEU Q 23 " pdb=" CD1 LEU Q 23 " pdb=" CD2 LEU Q 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PHE O 104 " pdb=" N PHE O 104 " pdb=" C PHE O 104 " pdb=" CB PHE O 104 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C3' DG J 253 " pdb=" C4' DG J 253 " pdb=" O3' DG J 253 " pdb=" C2' DG J 253 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2453 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 59 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C LYS L 59 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS L 59 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL L 60 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO M 80 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 60 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C VAL L 60 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL L 60 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE L 61 " -0.014 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2510 2.77 - 3.30: 12738 3.30 - 3.83: 30793 3.83 - 4.37: 34366 4.37 - 4.90: 46793 Nonbonded interactions: 127200 Sorted by model distance: nonbonded pdb=" O GLN O 93 " pdb=" OG SER O 96 " model vdw 2.234 3.040 nonbonded pdb=" OG SER M 40 " pdb=" O ARG M 42 " model vdw 2.258 3.040 nonbonded pdb=" O VAL N 111 " pdb=" OG1 THR N 115 " model vdw 2.266 3.040 nonbonded pdb=" O THR Q 16 " pdb=" OG SER Q 19 " model vdw 2.302 3.040 nonbonded pdb=" NE2 HIS K 113 " pdb=" OD1 ASP O 123 " model vdw 2.302 3.120 ... (remaining 127195 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 'K' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.150 Find NCS groups from input model: 0.130 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.007 0.045 14846 Z= 0.629 Angle : 1.016 15.456 21563 Z= 0.819 Chirality : 0.051 0.256 2456 Planarity : 0.006 0.068 1498 Dihedral : 30.285 179.340 6441 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.30 (0.27), residues: 825 helix: 0.59 (0.20), residues: 567 sheet: -1.82 (1.57), residues: 10 loop : -0.37 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 67 TYR 0.022 0.003 TYR N 37 PHE 0.040 0.003 PHE O 104 HIS 0.007 0.002 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.63 (14846) covalent geometry : angle 1.01649 / 0.82 (21563) hydrogen bonds : bond 0.11549 / 7.57 ( 892) hydrogen bonds : angle 4.84078 / 3.57 ( 2205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9476 (m-80) cc_final: 0.9199 (m-80) REVERT: K 120 MET cc_start: 0.8002 (tpp) cc_final: 0.7619 (tpp) REVERT: M 61 GLU cc_start: 0.9314 (pp20) cc_final: 0.9027 (pp20) REVERT: N 31 ARG cc_start: 0.7836 (mpp80) cc_final: 0.7583 (ttp80) REVERT: N 37 TYR cc_start: 0.9261 (m-10) cc_final: 0.8909 (m-10) REVERT: N 102 LEU cc_start: 0.8944 (tp) cc_final: 0.8665 (tp) REVERT: N 105 GLU cc_start: 0.9568 (tp30) cc_final: 0.9323 (tp30) REVERT: O 59 GLU cc_start: 0.9536 (tp30) cc_final: 0.9273 (pm20) REVERT: O 67 PHE cc_start: 0.9295 (t80) cc_final: 0.9070 (t80) REVERT: O 104 PHE cc_start: 0.9014 (m-80) cc_final: 0.8755 (m-10) REVERT: O 105 GLU cc_start: 0.9086 (mp0) cc_final: 0.8846 (mp0) REVERT: P 74 GLU cc_start: 0.9363 (pp20) cc_final: 0.9108 (pp20) REVERT: Q 56 GLU cc_start: 0.8992 (tt0) cc_final: 0.8477 (mt-10) REVERT: Q 64 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9360 (mm-30) REVERT: Q 95 LYS cc_start: 0.9136 (pptt) cc_final: 0.8496 (mmtt) REVERT: R 102 LEU cc_start: 0.9445 (mm) cc_final: 0.8887 (tp) REVERT: R 109 HIS cc_start: 0.9717 (m-70) cc_final: 0.9480 (m170) REVERT: R 113 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9402 (mm-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1086 time to fit residues: 19.1747 Evaluate side-chains 80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN R 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.025959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.020977 restraints weight = 236146.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.021621 restraints weight = 108745.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.022095 restraints weight = 64455.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.022390 restraints weight = 44218.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.022565 restraints weight = 33743.836| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14846 Z= 0.215 Angle : 0.770 7.743 21563 Z= 0.447 Chirality : 0.051 0.306 2456 Planarity : 0.006 0.057 1498 Dihedral : 33.988 178.089 4789 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 1.28 (0.27), residues: 825 helix: 1.40 (0.20), residues: 574 sheet: -2.26 (1.40), residues: 10 loop : -0.23 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 77 TYR 0.014 0.002 TYR L 88 PHE 0.018 0.002 PHE P 100 HIS 0.007 0.001 HIS R 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.21 (14846) covalent geometry : angle 0.76963 / 0.45 (21563) hydrogen bonds : bond 0.07766 / 5.17 ( 892) hydrogen bonds : angle 4.01203 / 2.95 ( 2205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9636 (m-80) cc_final: 0.9119 (m-80) REVERT: K 120 MET cc_start: 0.8336 (tpp) cc_final: 0.7935 (tpp) REVERT: N 37 TYR cc_start: 0.9287 (m-10) cc_final: 0.8921 (m-10) REVERT: N 62 MET cc_start: 0.9244 (mmp) cc_final: 0.8940 (mmm) REVERT: N 71 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8876 (mm-30) REVERT: N 105 GLU cc_start: 0.9504 (tp30) cc_final: 0.9215 (tp30) REVERT: O 59 GLU cc_start: 0.9408 (tp30) cc_final: 0.9189 (pm20) REVERT: O 97 GLU cc_start: 0.8849 (pm20) cc_final: 0.8581 (mp0) REVERT: O 104 PHE cc_start: 0.9386 (m-80) cc_final: 0.8999 (m-10) REVERT: O 106 ASP cc_start: 0.9235 (m-30) cc_final: 0.8995 (m-30) REVERT: O 120 MET cc_start: 0.7859 (mtt) cc_final: 0.7581 (mtt) REVERT: P 74 GLU cc_start: 0.9420 (pp20) cc_final: 0.9175 (pp20) REVERT: Q 56 GLU cc_start: 0.9177 (tt0) cc_final: 0.8652 (mt-10) REVERT: Q 95 LYS cc_start: 0.9179 (pptt) cc_final: 0.8444 (mmtt) REVERT: R 113 GLU cc_start: 0.9594 (mm-30) cc_final: 0.9308 (mm-30) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1048 time to fit residues: 15.3125 Evaluate side-chains 72 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 60 optimal weight: 4.9990 chunk 104 optimal weight: 30.0000 chunk 65 optimal weight: 0.9980 chunk 106 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.020296 restraints weight = 244681.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.020897 restraints weight = 113716.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.021357 restraints weight = 67371.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021640 restraints weight = 47236.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.021823 restraints weight = 35534.932| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14846 Z= 0.243 Angle : 0.764 7.953 21563 Z= 0.443 Chirality : 0.049 0.307 2456 Planarity : 0.006 0.069 1498 Dihedral : 34.002 179.207 4789 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.29 % Allowed : 4.33 % Favored : 95.38 % 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: 1.43 (0.28), residues: 825 helix: 1.51 (0.21), residues: 576 sheet: -2.61 (1.41), residues: 10 loop : -0.14 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 77 TYR 0.025 0.002 TYR R 42 PHE 0.021 0.003 PHE P 100 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.24 (14846) covalent geometry : angle 0.76425 / 0.44 (21563) hydrogen bonds : bond 0.09740 / 6.50 ( 892) hydrogen bonds : angle 4.00183 / 2.96 ( 2205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9630 (m-80) cc_final: 0.9150 (m-80) REVERT: K 120 MET cc_start: 0.8389 (tpp) cc_final: 0.8036 (tpp) REVERT: N 37 TYR cc_start: 0.9366 (m-10) cc_final: 0.9016 (m-10) REVERT: N 62 MET cc_start: 0.9276 (mmp) cc_final: 0.8931 (mmm) REVERT: N 71 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8921 (mm-30) REVERT: N 82 HIS cc_start: 0.9631 (t-90) cc_final: 0.9418 (t-90) REVERT: N 105 GLU cc_start: 0.9515 (tp30) cc_final: 0.9247 (tp30) REVERT: O 59 GLU cc_start: 0.9411 (tp30) cc_final: 0.9078 (pm20) REVERT: O 104 PHE cc_start: 0.9508 (m-10) cc_final: 0.9145 (m-80) REVERT: O 106 ASP cc_start: 0.9273 (m-30) cc_final: 0.9057 (m-30) REVERT: O 120 MET cc_start: 0.7600 (mtt) cc_final: 0.7373 (mtt) REVERT: P 74 GLU cc_start: 0.9424 (pp20) cc_final: 0.9205 (pp20) REVERT: P 84 MET cc_start: 0.9435 (pmm) cc_final: 0.9224 (pmm) REVERT: Q 56 GLU cc_start: 0.9216 (tt0) cc_final: 0.8437 (mt-10) REVERT: Q 95 LYS cc_start: 0.9294 (pptt) cc_final: 0.8570 (mmtt) REVERT: R 95 GLN cc_start: 0.9697 (pt0) cc_final: 0.9381 (pp30) REVERT: R 102 LEU cc_start: 0.9477 (mm) cc_final: 0.8781 (tp) outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.1109 time to fit residues: 15.1497 Evaluate side-chains 71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 105 optimal weight: 30.0000 chunk 44 optimal weight: 0.0070 chunk 83 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.026048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.021020 restraints weight = 235132.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.021673 restraints weight = 111023.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.022187 restraints weight = 65466.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022498 restraints weight = 44455.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.022682 restraints weight = 33338.228| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14846 Z= 0.157 Angle : 0.692 7.181 21563 Z= 0.405 Chirality : 0.048 0.330 2456 Planarity : 0.005 0.061 1498 Dihedral : 33.946 179.991 4789 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 1.75 (0.28), residues: 825 helix: 1.77 (0.21), residues: 576 sheet: -2.93 (1.31), residues: 10 loop : -0.07 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 29 TYR 0.011 0.001 TYR N 37 PHE 0.010 0.002 PHE M 25 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.16 (14846) covalent geometry : angle 0.69173 / 0.41 (21563) hydrogen bonds : bond 0.05930 / 3.89 ( 892) hydrogen bonds : angle 3.75984 / 2.79 ( 2205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9607 (m-80) cc_final: 0.9113 (m-80) REVERT: K 105 GLU cc_start: 0.9137 (mp0) cc_final: 0.8874 (mp0) REVERT: K 120 MET cc_start: 0.8415 (tpp) cc_final: 0.8077 (tpp) REVERT: L 63 GLU cc_start: 0.9619 (pm20) cc_final: 0.9343 (pm20) REVERT: N 37 TYR cc_start: 0.9347 (m-10) cc_final: 0.8954 (m-10) REVERT: N 62 MET cc_start: 0.9291 (mmp) cc_final: 0.9022 (mmp) REVERT: N 71 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8945 (pp20) REVERT: N 82 HIS cc_start: 0.9645 (t-90) cc_final: 0.9429 (t-90) REVERT: N 102 LEU cc_start: 0.9054 (tp) cc_final: 0.8690 (tp) REVERT: N 105 GLU cc_start: 0.9544 (tp30) cc_final: 0.9264 (tp30) REVERT: O 59 GLU cc_start: 0.9459 (tp30) cc_final: 0.9111 (pm20) REVERT: O 104 PHE cc_start: 0.9453 (m-10) cc_final: 0.9042 (m-80) REVERT: O 106 ASP cc_start: 0.9310 (m-30) cc_final: 0.9097 (m-30) REVERT: O 120 MET cc_start: 0.7462 (mtt) cc_final: 0.7206 (mtt) REVERT: P 74 GLU cc_start: 0.9355 (pp20) cc_final: 0.9094 (pp20) REVERT: P 84 MET cc_start: 0.9407 (pmm) cc_final: 0.9200 (pmm) REVERT: Q 56 GLU cc_start: 0.9154 (tt0) cc_final: 0.8357 (mt-10) REVERT: Q 61 GLU cc_start: 0.9437 (pp20) cc_final: 0.9019 (pp20) REVERT: R 95 GLN cc_start: 0.9646 (pt0) cc_final: 0.9355 (pp30) REVERT: R 102 LEU cc_start: 0.9424 (mm) cc_final: 0.8772 (tp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1082 time to fit residues: 15.9023 Evaluate side-chains 73 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 30.0000 chunk 105 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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 = 0.2870 r_free = 0.2870 target = 0.025686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.020777 restraints weight = 240469.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.021418 restraints weight = 110376.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.021918 restraints weight = 64753.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.022216 restraints weight = 43448.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.022388 restraints weight = 33301.095| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14846 Z= 0.195 Angle : 0.715 9.237 21563 Z= 0.414 Chirality : 0.047 0.318 2456 Planarity : 0.005 0.061 1498 Dihedral : 33.884 179.694 4789 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 1.71 (0.28), residues: 825 helix: 1.74 (0.21), residues: 576 sheet: -3.16 (1.30), residues: 10 loop : -0.06 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG M 20 TYR 0.018 0.002 TYR L 98 PHE 0.021 0.002 PHE M 25 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.19 (14846) covalent geometry : angle 0.71527 / 0.41 (21563) hydrogen bonds : bond 0.07449 / 4.95 ( 892) hydrogen bonds : angle 3.78464 / 2.79 ( 2205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9334 (tp30) cc_final: 0.9008 (tp30) REVERT: K 104 PHE cc_start: 0.9624 (m-80) cc_final: 0.9149 (m-80) REVERT: K 120 MET cc_start: 0.8513 (tpp) cc_final: 0.8201 (tpp) REVERT: N 37 TYR cc_start: 0.9367 (m-10) cc_final: 0.8954 (m-10) REVERT: N 57 LYS cc_start: 0.8780 (pptt) cc_final: 0.8508 (ptmt) REVERT: N 62 MET cc_start: 0.9277 (mmp) cc_final: 0.8952 (mmm) REVERT: N 71 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8947 (pp20) REVERT: N 105 GLU cc_start: 0.9519 (tp30) cc_final: 0.9240 (tp30) REVERT: O 59 GLU cc_start: 0.9397 (tp30) cc_final: 0.9043 (pm20) REVERT: O 104 PHE cc_start: 0.9505 (m-10) cc_final: 0.8987 (m-80) REVERT: O 105 GLU cc_start: 0.9007 (mp0) cc_final: 0.8677 (mm-30) REVERT: O 106 ASP cc_start: 0.9275 (m-30) cc_final: 0.9052 (m-30) REVERT: O 120 MET cc_start: 0.7490 (mtt) cc_final: 0.7215 (mtt) REVERT: P 74 GLU cc_start: 0.9382 (pp20) cc_final: 0.9147 (pp20) REVERT: P 84 MET cc_start: 0.9381 (pmm) cc_final: 0.9171 (pmm) REVERT: Q 56 GLU cc_start: 0.9180 (tt0) cc_final: 0.8360 (mt-10) REVERT: Q 61 GLU cc_start: 0.9466 (pp20) cc_final: 0.9062 (pp20) REVERT: R 95 GLN cc_start: 0.9658 (pt0) cc_final: 0.9365 (pp30) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1066 time to fit residues: 15.7205 Evaluate side-chains 70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 59 optimal weight: 0.3980 chunk 38 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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 = 0.2855 r_free = 0.2855 target = 0.025231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.020435 restraints weight = 243302.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.021045 restraints weight = 113009.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.021507 restraints weight = 66459.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.021816 restraints weight = 46091.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.021933 restraints weight = 34154.954| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14846 Z= 0.215 Angle : 0.727 7.418 21563 Z= 0.420 Chirality : 0.047 0.327 2456 Planarity : 0.005 0.059 1498 Dihedral : 33.928 179.884 4789 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.43 % Allowed : 1.73 % Favored : 97.84 % 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: 1.60 (0.28), residues: 825 helix: 1.63 (0.21), residues: 576 sheet: -3.45 (1.32), residues: 10 loop : 0.01 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 77 TYR 0.012 0.001 TYR R 121 PHE 0.014 0.002 PHE O 67 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.21 (14846) covalent geometry : angle 0.72712 / 0.42 (21563) hydrogen bonds : bond 0.08408 / 5.59 ( 892) hydrogen bonds : angle 3.86731 / 2.85 ( 2205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9366 (tp30) cc_final: 0.9086 (tp30) REVERT: K 104 PHE cc_start: 0.9640 (m-80) cc_final: 0.9204 (m-80) REVERT: K 120 MET cc_start: 0.8556 (tpp) cc_final: 0.8272 (tpp) REVERT: N 37 TYR cc_start: 0.9417 (m-10) cc_final: 0.9027 (m-10) REVERT: N 62 MET cc_start: 0.9303 (mmp) cc_final: 0.8944 (mmm) REVERT: N 71 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8943 (pp20) REVERT: N 105 GLU cc_start: 0.9513 (tp30) cc_final: 0.9256 (tp30) REVERT: O 59 GLU cc_start: 0.9419 (tp30) cc_final: 0.9032 (pm20) REVERT: O 104 PHE cc_start: 0.9549 (m-10) cc_final: 0.9157 (m-80) REVERT: O 105 GLU cc_start: 0.9115 (mp0) cc_final: 0.8789 (mp0) REVERT: O 106 ASP cc_start: 0.9309 (m-30) cc_final: 0.9088 (m-30) REVERT: O 120 MET cc_start: 0.7452 (mtt) cc_final: 0.7150 (mmm) REVERT: P 74 GLU cc_start: 0.9374 (pp20) cc_final: 0.9138 (pp20) REVERT: P 84 MET cc_start: 0.9378 (pmm) cc_final: 0.9168 (pmm) REVERT: Q 56 GLU cc_start: 0.9178 (tt0) cc_final: 0.8340 (mt-10) REVERT: R 59 MET cc_start: 0.9216 (tmm) cc_final: 0.8885 (tpp) REVERT: R 95 GLN cc_start: 0.9673 (pt0) cc_final: 0.9357 (pp30) REVERT: R 102 LEU cc_start: 0.9475 (mm) cc_final: 0.9130 (mp) outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.0990 time to fit residues: 14.6467 Evaluate side-chains 71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 94 optimal weight: 40.0000 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 93 GLN Q 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.025226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.020404 restraints weight = 243388.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.021044 restraints weight = 113614.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.021509 restraints weight = 67269.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.021797 restraints weight = 45723.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.021978 restraints weight = 34668.377| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14846 Z= 0.211 Angle : 0.731 9.902 21563 Z= 0.420 Chirality : 0.047 0.340 2456 Planarity : 0.005 0.062 1498 Dihedral : 33.943 179.795 4789 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 1.68 (0.28), residues: 825 helix: 1.68 (0.21), residues: 574 sheet: -3.44 (1.38), residues: 10 loop : 0.06 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 69 TYR 0.015 0.002 TYR R 121 PHE 0.010 0.002 PHE O 67 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.21 (14846) covalent geometry : angle 0.73114 / 0.42 (21563) hydrogen bonds : bond 0.08165 / 5.43 ( 892) hydrogen bonds : angle 3.94003 / 2.91 ( 2205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9358 (tp30) cc_final: 0.9064 (tp30) REVERT: K 104 PHE cc_start: 0.9624 (m-80) cc_final: 0.9188 (m-80) REVERT: K 120 MET cc_start: 0.8617 (tpp) cc_final: 0.8341 (tpp) REVERT: N 37 TYR cc_start: 0.9396 (m-10) cc_final: 0.9038 (m-10) REVERT: N 62 MET cc_start: 0.9327 (mmp) cc_final: 0.8954 (mmm) REVERT: N 71 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8937 (pp20) REVERT: N 105 GLU cc_start: 0.9527 (tp30) cc_final: 0.9254 (tp30) REVERT: O 59 GLU cc_start: 0.9382 (tp30) cc_final: 0.8967 (pm20) REVERT: O 104 PHE cc_start: 0.9544 (m-10) cc_final: 0.9199 (m-80) REVERT: O 106 ASP cc_start: 0.9278 (m-30) cc_final: 0.9068 (m-30) REVERT: O 120 MET cc_start: 0.7393 (mtt) cc_final: 0.7168 (mmm) REVERT: P 74 GLU cc_start: 0.9388 (pp20) cc_final: 0.9146 (pp20) REVERT: Q 56 GLU cc_start: 0.9171 (tt0) cc_final: 0.8313 (mt-10) REVERT: R 59 MET cc_start: 0.9172 (tmm) cc_final: 0.8916 (tpp) REVERT: R 102 LEU cc_start: 0.9478 (mm) cc_final: 0.9238 (mp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1029 time to fit residues: 14.7950 Evaluate side-chains 67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 40.0000 chunk 74 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.025072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.020285 restraints weight = 244686.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.020917 restraints weight = 115250.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.021416 restraints weight = 67678.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.021711 restraints weight = 44947.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.021873 restraints weight = 34600.453| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14846 Z= 0.219 Angle : 0.740 7.426 21563 Z= 0.426 Chirality : 0.047 0.352 2456 Planarity : 0.005 0.062 1498 Dihedral : 33.968 179.622 4789 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 1.45 (0.28), residues: 825 helix: 1.46 (0.21), residues: 586 sheet: -3.60 (1.25), residues: 10 loop : 0.06 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 77 TYR 0.011 0.001 TYR R 121 PHE 0.012 0.002 PHE O 78 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.22 (14846) covalent geometry : angle 0.74035 / 0.43 (21563) hydrogen bonds : bond 0.08499 / 5.65 ( 892) hydrogen bonds : angle 4.02965 / 2.97 ( 2205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9366 (tp30) cc_final: 0.9061 (tp30) REVERT: K 104 PHE cc_start: 0.9646 (m-80) cc_final: 0.9182 (m-80) REVERT: K 120 MET cc_start: 0.8624 (tpp) cc_final: 0.8285 (tpp) REVERT: N 37 TYR cc_start: 0.9408 (m-10) cc_final: 0.9053 (m-10) REVERT: N 62 MET cc_start: 0.9343 (mmp) cc_final: 0.8954 (mmm) REVERT: N 71 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8936 (pp20) REVERT: N 105 GLU cc_start: 0.9529 (tp30) cc_final: 0.9272 (tp30) REVERT: O 59 GLU cc_start: 0.9404 (tp30) cc_final: 0.9169 (tp30) REVERT: O 104 PHE cc_start: 0.9560 (m-10) cc_final: 0.9130 (m-80) REVERT: O 105 GLU cc_start: 0.9058 (mp0) cc_final: 0.8761 (mm-30) REVERT: O 106 ASP cc_start: 0.9303 (m-30) cc_final: 0.9082 (m-30) REVERT: P 74 GLU cc_start: 0.9384 (pp20) cc_final: 0.9150 (pp20) REVERT: Q 56 GLU cc_start: 0.9171 (tt0) cc_final: 0.8315 (mt-10) REVERT: R 102 LEU cc_start: 0.9503 (mm) cc_final: 0.9183 (mp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1060 time to fit residues: 14.8290 Evaluate side-chains 67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 40.0000 chunk 76 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.025697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.020810 restraints weight = 240098.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.021453 restraints weight = 111242.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.021946 restraints weight = 65382.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.022263 restraints weight = 44133.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022499 restraints weight = 33229.932| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14846 Z= 0.169 Angle : 0.715 10.437 21563 Z= 0.412 Chirality : 0.047 0.366 2456 Planarity : 0.005 0.063 1498 Dihedral : 33.887 179.659 4789 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.29), residues: 825 helix: 1.59 (0.21), residues: 584 sheet: -3.66 (1.22), residues: 10 loop : -0.02 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 69 TYR 0.017 0.001 TYR R 121 PHE 0.012 0.002 PHE P 61 HIS 0.004 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.17 (14846) covalent geometry : angle 0.71498 / 0.41 (21563) hydrogen bonds : bond 0.06136 / 4.04 ( 892) hydrogen bonds : angle 3.86373 / 2.85 ( 2205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9357 (tp30) cc_final: 0.9028 (tp30) REVERT: K 104 PHE cc_start: 0.9569 (m-80) cc_final: 0.9145 (m-80) REVERT: K 120 MET cc_start: 0.8630 (tpp) cc_final: 0.8274 (tpp) REVERT: L 63 GLU cc_start: 0.9591 (pm20) cc_final: 0.9323 (pm20) REVERT: L 68 ASP cc_start: 0.9367 (m-30) cc_final: 0.9130 (m-30) REVERT: N 37 TYR cc_start: 0.9343 (m-10) cc_final: 0.8995 (m-10) REVERT: N 62 MET cc_start: 0.9328 (mmp) cc_final: 0.8945 (mmm) REVERT: N 71 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8956 (pp20) REVERT: N 100 LEU cc_start: 0.9405 (mt) cc_final: 0.9186 (mt) REVERT: N 102 LEU cc_start: 0.9083 (tp) cc_final: 0.8730 (tp) REVERT: N 105 GLU cc_start: 0.9521 (tp30) cc_final: 0.9257 (tp30) REVERT: O 59 GLU cc_start: 0.9386 (tp30) cc_final: 0.8983 (pm20) REVERT: O 104 PHE cc_start: 0.9516 (m-10) cc_final: 0.9161 (m-80) REVERT: O 105 GLU cc_start: 0.9071 (mp0) cc_final: 0.8799 (mp0) REVERT: O 106 ASP cc_start: 0.9296 (m-30) cc_final: 0.9010 (m-30) REVERT: O 120 MET cc_start: 0.8713 (mmp) cc_final: 0.8267 (mmt) REVERT: P 74 GLU cc_start: 0.9335 (pp20) cc_final: 0.9093 (pp20) REVERT: Q 56 GLU cc_start: 0.9193 (tt0) cc_final: 0.8318 (mt-10) REVERT: Q 61 GLU cc_start: 0.9408 (pp20) cc_final: 0.9081 (pp20) REVERT: Q 95 LYS cc_start: 0.8895 (pptt) cc_final: 0.7878 (tptt) REVERT: R 105 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8381 (tm-30) REVERT: R 109 HIS cc_start: 0.9544 (m90) cc_final: 0.9087 (m170) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1031 time to fit residues: 15.5670 Evaluate side-chains 73 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 30.0000 chunk 111 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 50.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.2897 r_free = 0.2897 target = 0.026309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.021367 restraints weight = 233194.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.022038 restraints weight = 107496.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022557 restraints weight = 62674.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.022864 restraints weight = 42470.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.022995 restraints weight = 31555.101| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14846 Z= 0.152 Angle : 0.704 7.752 21563 Z= 0.406 Chirality : 0.046 0.368 2456 Planarity : 0.005 0.063 1498 Dihedral : 33.704 179.673 4789 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.61 (0.29), residues: 825 helix: 1.60 (0.21), residues: 584 sheet: -3.67 (1.16), residues: 10 loop : 0.05 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 92 TYR 0.014 0.001 TYR R 42 PHE 0.018 0.002 PHE K 78 HIS 0.005 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (14846) covalent geometry : angle 0.70431 / 0.41 (21563) hydrogen bonds : bond 0.04966 / 3.26 ( 892) hydrogen bonds : angle 3.79586 / 2.81 ( 2205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9387 (tp30) cc_final: 0.9022 (tp30) REVERT: K 104 PHE cc_start: 0.9548 (m-80) cc_final: 0.9105 (m-80) REVERT: K 120 MET cc_start: 0.8598 (tpp) cc_final: 0.8253 (tpp) REVERT: L 63 GLU cc_start: 0.9546 (pm20) cc_final: 0.9325 (pm20) REVERT: N 37 TYR cc_start: 0.9351 (m-10) cc_final: 0.9005 (m-10) REVERT: N 62 MET cc_start: 0.9337 (mmp) cc_final: 0.8930 (mmm) REVERT: N 71 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8948 (pp20) REVERT: N 102 LEU cc_start: 0.9029 (tp) cc_final: 0.8672 (tp) REVERT: N 105 GLU cc_start: 0.9562 (tp30) cc_final: 0.9331 (tp30) REVERT: O 59 GLU cc_start: 0.9446 (tp30) cc_final: 0.9050 (tp30) REVERT: O 104 PHE cc_start: 0.9456 (m-10) cc_final: 0.9023 (m-80) REVERT: O 105 GLU cc_start: 0.9008 (mp0) cc_final: 0.8747 (mp0) REVERT: O 106 ASP cc_start: 0.9310 (m-30) cc_final: 0.9072 (m-30) REVERT: P 74 GLU cc_start: 0.9312 (pp20) cc_final: 0.9063 (pp20) REVERT: Q 56 GLU cc_start: 0.9184 (tt0) cc_final: 0.8297 (mt-10) REVERT: Q 61 GLU cc_start: 0.9401 (pp20) cc_final: 0.9065 (pp20) REVERT: Q 64 GLU cc_start: 0.9641 (mm-30) cc_final: 0.9264 (mm-30) REVERT: Q 95 LYS cc_start: 0.8891 (pptt) cc_final: 0.7907 (tptt) REVERT: R 102 LEU cc_start: 0.9458 (mm) cc_final: 0.8786 (tp) REVERT: R 105 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8555 (tm-30) REVERT: R 109 HIS cc_start: 0.9589 (m90) cc_final: 0.9022 (m90) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1091 time to fit residues: 17.4007 Evaluate side-chains 78 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 81 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.2857 r_free = 0.2857 target = 0.025185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.020473 restraints weight = 247601.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.021087 restraints weight = 116000.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.021577 restraints weight = 68324.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.021759 restraints weight = 45751.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.021958 restraints weight = 37053.700| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14846 Z= 0.223 Angle : 0.747 10.333 21563 Z= 0.425 Chirality : 0.047 0.358 2456 Planarity : 0.005 0.067 1498 Dihedral : 33.788 179.978 4789 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.57 (0.29), residues: 825 helix: 1.57 (0.21), residues: 584 sheet: -3.70 (1.18), residues: 10 loop : 0.03 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 69 TYR 0.016 0.002 TYR R 121 PHE 0.010 0.002 PHE L 100 HIS 0.009 0.002 HIS Q 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.22 (14846) covalent geometry : angle 0.74704 / 0.43 (21563) hydrogen bonds : bond 0.08962 / 5.97 ( 892) hydrogen bonds : angle 4.02809 / 3.00 ( 2205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.52 seconds wall clock time: 29 minutes 30.17 seconds (1770.17 seconds total)