Starting phenix.real_space_refine on Fri Jul 3 18:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfx_13383/07_2026/7pfx_13383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfx_13383/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pfx_13383/07_2026/7pfx_13383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfx_13383/07_2026/7pfx_13383.map" model { file = "/net/cci-nas-00/data/ceres_data/7pfx_13383/07_2026/7pfx_13383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfx_13383/07_2026/7pfx_13383.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.21, 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: 0.84 Conformation dependent library (CDL) restraints added in 247.6 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: 1.73 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: 2.66 Time building geometry restraints manager: 1.13 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: 21293 3.09 - 6.18: 242 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.110 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- 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= 0.628 Angle : 1.008 15.456 21563 Z= 0.811 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 1.00833 / 0.81 (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 : 0.279 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: 0.7489 (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: 0.8476 (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: 0.8497 (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: 0.0876 time to fit residues: 15.6783 Evaluate side-chains 79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 20.0000 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: 20.0000 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 = 0.2881 r_free = 0.2881 target = 0.026001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.021013 restraints weight = 235883.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.021662 restraints weight = 108697.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.022125 restraints weight = 64250.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.022434 restraints weight = 43980.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.022620 restraints weight = 33299.894| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14846 Z= 0.218 Angle : 0.760 7.404 21563 Z= 0.442 Chirality : 0.051 0.292 2456 Planarity : 0.006 0.068 1498 Dihedral : 34.049 176.763 4789 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 825 helix: 1.38 (0.20), residues: 574 sheet: -2.27 (1.40), residues: 10 loop : -0.24 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 77 TYR 0.013 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 0.00354 / 0.22 (14846) covalent geometry : angle 0.76016 / 0.44 (21563) hydrogen bonds : bond 0.07763 / 5.18 ( 892) hydrogen bonds : angle 4.02035 / 2.96 ( 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 96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.345 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 104 PHE cc_start: 0.9636 (m-80) cc_final: 0.9120 (m-80) REVERT: K 120 MET cc_start: 0.8343 (tpp) cc_final: 0.7961 (tpp) REVERT: N 37 TYR cc_start: 0.9287 (m-10) cc_final: 0.8969 (m-10) REVERT: N 62 MET cc_start: 0.9272 (mmp) cc_final: 0.8940 (mmm) REVERT: N 71 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8903 (mm-30) REVERT: N 105 GLU cc_start: 0.9505 (tp30) cc_final: 0.9216 (tp30) REVERT: O 59 GLU cc_start: 0.9409 (tp30) cc_final: 0.9191 (pm20) REVERT: O 104 PHE cc_start: 0.9385 (m-80) cc_final: 0.9007 (m-10) REVERT: O 106 ASP cc_start: 0.9237 (m-30) cc_final: 0.8996 (m-30) REVERT: O 120 MET cc_start: 0.7983 (mtt) cc_final: 0.7729 (mtt) REVERT: P 74 GLU cc_start: 0.9432 (pp20) cc_final: 0.9189 (pp20) REVERT: Q 56 GLU cc_start: 0.9175 (tt0) cc_final: 0.8654 (mt-10) REVERT: Q 95 LYS cc_start: 0.9190 (pptt) cc_final: 0.8440 (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: 96 average time/residue: 0.0996 time to fit residues: 14.3295 Evaluate side-chains 71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.024951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.020137 restraints weight = 248140.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.020742 restraints weight = 116111.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.021166 restraints weight = 69327.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.021471 restraints weight = 47550.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.021659 restraints weight = 36427.012| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14846 Z= 0.263 Angle : 0.766 8.215 21563 Z= 0.448 Chirality : 0.049 0.295 2456 Planarity : 0.006 0.068 1498 Dihedral : 34.115 179.501 4789 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: 1.34 (0.28), residues: 825 helix: 1.44 (0.21), residues: 576 sheet: -2.65 (1.44), residues: 10 loop : -0.15 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 77 TYR 0.017 0.002 TYR R 40 PHE 0.021 0.003 PHE P 100 HIS 0.006 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.26 (14846) covalent geometry : angle 0.76583 / 0.45 (21563) hydrogen bonds : bond 0.10447 / 6.97 ( 892) hydrogen bonds : angle 4.11095 / 3.05 ( 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 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.253 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: 0.9632 (m-80) cc_final: 0.9156 (m-80) REVERT: K 120 MET cc_start: 0.8421 (tpp) cc_final: 0.8069 (tpp) REVERT: N 37 TYR cc_start: 0.9381 (m-10) cc_final: 0.9014 (m-10) REVERT: N 62 MET cc_start: 0.9267 (mmp) cc_final: 0.8914 (mmm) REVERT: N 71 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8929 (mm-30) REVERT: N 82 HIS cc_start: 0.9632 (t-90) cc_final: 0.9420 (t-90) REVERT: N 105 GLU cc_start: 0.9506 (tp30) cc_final: 0.9229 (tp30) REVERT: O 59 GLU cc_start: 0.9396 (tp30) cc_final: 0.9059 (pm20) REVERT: O 104 PHE cc_start: 0.9517 (m-10) cc_final: 0.9156 (m-80) REVERT: O 106 ASP cc_start: 0.9267 (m-30) cc_final: 0.9049 (m-30) REVERT: O 120 MET cc_start: 0.7607 (mtt) cc_final: 0.7367 (mtt) REVERT: P 74 GLU cc_start: 0.9432 (pp20) cc_final: 0.9222 (pp20) REVERT: P 84 MET cc_start: 0.9415 (pmm) cc_final: 0.9201 (pmm) REVERT: Q 56 GLU cc_start: 0.9224 (tt0) cc_final: 0.8478 (mt-10) REVERT: Q 95 LYS cc_start: 0.9290 (pptt) cc_final: 0.8560 (mmtt) REVERT: R 95 GLN cc_start: 0.9700 (pt0) cc_final: 0.9372 (pp30) REVERT: R 102 LEU cc_start: 0.9490 (mm) cc_final: 0.8798 (tp) REVERT: R 109 HIS cc_start: 0.9565 (m90) cc_final: 0.9244 (m90) REVERT: R 113 GLU cc_start: 0.9602 (mm-30) cc_final: 0.9327 (mm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0910 time to fit residues: 12.3587 Evaluate side-chains 71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.9990 chunk 100 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 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: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- 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 = 0.2890 r_free = 0.2890 target = 0.026172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.021124 restraints weight = 234026.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.021781 restraints weight = 109353.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.022316 restraints weight = 64923.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.022611 restraints weight = 43553.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.022756 restraints weight = 32698.788| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14846 Z= 0.156 Angle : 0.683 7.622 21563 Z= 0.405 Chirality : 0.047 0.320 2456 Planarity : 0.005 0.060 1498 Dihedral : 34.044 178.717 4789 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 1.69 (0.28), residues: 825 helix: 1.75 (0.21), residues: 576 sheet: -2.92 (1.30), residues: 10 loop : -0.18 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 29 TYR 0.023 0.002 TYR R 42 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 0.00241 / 0.16 (14846) covalent geometry : angle 0.68270 / 0.40 (21563) hydrogen bonds : bond 0.05466 / 3.57 ( 892) hydrogen bonds : angle 3.74420 / 2.76 ( 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 : 0.227 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 104 PHE cc_start: 0.9607 (m-80) cc_final: 0.9112 (m-80) REVERT: K 105 GLU cc_start: 0.9162 (mp0) cc_final: 0.8888 (mp0) REVERT: K 120 MET cc_start: 0.8434 (tpp) cc_final: 0.8098 (tpp) REVERT: L 63 GLU cc_start: 0.9606 (pm20) cc_final: 0.9310 (pm20) REVERT: N 37 TYR cc_start: 0.9340 (m-10) cc_final: 0.8950 (m-10) REVERT: N 62 MET cc_start: 0.9284 (mmp) cc_final: 0.9016 (mmp) REVERT: N 71 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8941 (pp20) REVERT: N 82 HIS cc_start: 0.9644 (t-90) cc_final: 0.9429 (t-90) REVERT: N 102 LEU cc_start: 0.9064 (tp) cc_final: 0.8706 (tp) REVERT: N 105 GLU cc_start: 0.9547 (tp30) cc_final: 0.9270 (tp30) REVERT: O 59 GLU cc_start: 0.9437 (tp30) cc_final: 0.9124 (pm20) REVERT: O 104 PHE cc_start: 0.9473 (m-10) cc_final: 0.8972 (m-80) REVERT: O 105 GLU cc_start: 0.9087 (mp0) cc_final: 0.8791 (mm-30) REVERT: O 106 ASP cc_start: 0.9285 (m-30) cc_final: 0.9061 (m-30) REVERT: O 120 MET cc_start: 0.7444 (mtt) cc_final: 0.7195 (mtt) REVERT: P 74 GLU cc_start: 0.9354 (pp20) cc_final: 0.9072 (pp20) REVERT: Q 56 GLU cc_start: 0.9135 (tt0) cc_final: 0.8408 (mt-10) REVERT: R 95 GLN cc_start: 0.9651 (pt0) cc_final: 0.9369 (pp30) REVERT: R 102 LEU cc_start: 0.9427 (mm) cc_final: 0.8775 (tp) REVERT: R 113 GLU cc_start: 0.9625 (mm-30) cc_final: 0.9310 (mm-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1017 time to fit residues: 14.8093 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 : 0.372 ------------------------------------------------------------------------------- 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: 6.9990 chunk 93 optimal weight: 30.0000 chunk 105 optimal weight: 30.0000 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.026266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.021255 restraints weight = 237660.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021899 restraints weight = 111699.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.022419 restraints weight = 66143.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.022698 restraints weight = 44494.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.022908 restraints weight = 34424.537| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14846 Z= 0.152 Angle : 0.675 9.275 21563 Z= 0.396 Chirality : 0.046 0.307 2456 Planarity : 0.004 0.058 1498 Dihedral : 33.921 178.624 4789 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % 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: 1.68 (0.28), residues: 825 helix: 1.73 (0.21), residues: 586 sheet: -3.16 (1.27), residues: 10 loop : -0.18 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 20 TYR 0.013 0.001 TYR R 121 PHE 0.022 0.002 PHE M 25 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.15 (14846) covalent geometry : angle 0.67508 / 0.40 (21563) hydrogen bonds : bond 0.05613 / 3.70 ( 892) hydrogen bonds : angle 3.65553 / 2.70 ( 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 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.280 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 104 PHE cc_start: 0.9605 (m-80) cc_final: 0.9141 (m-80) REVERT: K 120 MET cc_start: 0.8452 (tpp) cc_final: 0.8141 (tpp) REVERT: N 37 TYR cc_start: 0.9364 (m-10) cc_final: 0.8977 (m-10) REVERT: N 62 MET cc_start: 0.9294 (mmp) cc_final: 0.8973 (mmm) REVERT: N 71 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8934 (pp20) REVERT: N 82 HIS cc_start: 0.9641 (t-90) cc_final: 0.9415 (t70) REVERT: N 102 LEU cc_start: 0.9025 (tp) cc_final: 0.8631 (tp) REVERT: N 105 GLU cc_start: 0.9549 (tp30) cc_final: 0.9279 (tp30) REVERT: O 59 GLU cc_start: 0.9416 (tp30) cc_final: 0.9093 (pm20) REVERT: O 104 PHE cc_start: 0.9472 (m-10) cc_final: 0.8984 (m-80) REVERT: O 106 ASP cc_start: 0.9321 (m-30) cc_final: 0.9083 (m-30) REVERT: P 74 GLU cc_start: 0.9352 (pp20) cc_final: 0.9106 (pp20) REVERT: Q 56 GLU cc_start: 0.9111 (tt0) cc_final: 0.8355 (mt-10) REVERT: R 95 GLN cc_start: 0.9632 (pt0) cc_final: 0.9365 (pp30) REVERT: R 109 HIS cc_start: 0.9604 (m90) cc_final: 0.9303 (m90) REVERT: R 113 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9315 (mm-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0994 time to fit residues: 15.1326 Evaluate side-chains 74 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 106 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.021334 restraints weight = 236525.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.021984 restraints weight = 110576.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.022513 restraints weight = 65217.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.022794 restraints weight = 43839.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.022989 restraints weight = 34143.716| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14846 Z= 0.155 Angle : 0.663 6.619 21563 Z= 0.390 Chirality : 0.045 0.303 2456 Planarity : 0.004 0.058 1498 Dihedral : 33.819 179.460 4789 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.29 % Allowed : 1.59 % Favored : 98.12 % 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: 586 sheet: -3.14 (1.29), residues: 10 loop : -0.12 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 72 TYR 0.009 0.001 TYR N 37 PHE 0.014 0.002 PHE R 65 HIS 0.003 0.001 HIS K 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (14846) covalent geometry : angle 0.66275 / 0.39 (21563) hydrogen bonds : bond 0.05598 / 3.70 ( 892) hydrogen bonds : angle 3.57081 / 2.62 ( 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 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9381 (tp30) cc_final: 0.9024 (tp30) REVERT: K 104 PHE cc_start: 0.9605 (m-80) cc_final: 0.9141 (m-80) REVERT: K 120 MET cc_start: 0.8497 (tpp) cc_final: 0.8210 (tpp) REVERT: L 63 GLU cc_start: 0.9606 (pm20) cc_final: 0.9371 (pm20) REVERT: N 37 TYR cc_start: 0.9382 (m-10) cc_final: 0.9030 (m-10) REVERT: N 62 MET cc_start: 0.9326 (mmp) cc_final: 0.8983 (mmm) REVERT: N 71 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8935 (pp20) REVERT: N 82 HIS cc_start: 0.9629 (t-90) cc_final: 0.9416 (t70) REVERT: N 102 LEU cc_start: 0.8995 (tp) cc_final: 0.8645 (tp) REVERT: N 105 GLU cc_start: 0.9550 (tp30) cc_final: 0.9283 (tp30) REVERT: O 59 GLU cc_start: 0.9417 (tp30) cc_final: 0.9102 (pm20) REVERT: O 104 PHE cc_start: 0.9359 (m-10) cc_final: 0.8859 (m-80) REVERT: O 105 GLU cc_start: 0.9062 (mp0) cc_final: 0.8760 (mm-30) REVERT: O 106 ASP cc_start: 0.9321 (m-30) cc_final: 0.9117 (m-30) REVERT: P 74 GLU cc_start: 0.9349 (pp20) cc_final: 0.9109 (pp20) REVERT: Q 56 GLU cc_start: 0.9071 (tt0) cc_final: 0.8295 (mt-10) REVERT: R 95 GLN cc_start: 0.9640 (pt0) cc_final: 0.9361 (pp30) REVERT: R 108 LYS cc_start: 0.9700 (ptpp) cc_final: 0.9488 (ptpt) REVERT: R 109 HIS cc_start: 0.9611 (m90) cc_final: 0.9324 (m90) REVERT: R 113 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9321 (mm-30) outliers start: 2 outliers final: 1 residues processed: 99 average time/residue: 0.0912 time to fit residues: 13.8422 Evaluate side-chains 73 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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: 20.0000 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 40.0000 chunk 100 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 55 GLN P 93 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.020337 restraints weight = 244157.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.020997 restraints weight = 114864.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.021435 restraints weight = 68227.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.021712 restraints weight = 46878.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.021892 restraints weight = 35557.511| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2117 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= 0.236 Angle : 0.734 10.016 21563 Z= 0.424 Chirality : 0.046 0.305 2456 Planarity : 0.005 0.063 1498 Dihedral : 33.919 179.327 4789 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: 1.55 (0.28), residues: 825 helix: 1.56 (0.21), residues: 588 sheet: -3.32 (1.37), residues: 10 loop : -0.04 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 77 TYR 0.016 0.002 TYR R 121 PHE 0.012 0.002 PHE L 100 HIS 0.007 0.002 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.24 (14846) covalent geometry : angle 0.73399 / 0.42 (21563) hydrogen bonds : bond 0.09532 / 6.37 ( 892) hydrogen bonds : angle 3.92643 / 2.90 ( 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 92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9367 (tp30) cc_final: 0.9110 (tp30) REVERT: K 104 PHE cc_start: 0.9644 (m-80) cc_final: 0.9206 (m-80) REVERT: K 120 MET cc_start: 0.8553 (tpp) cc_final: 0.8209 (tpp) REVERT: N 37 TYR cc_start: 0.9427 (m-10) cc_final: 0.9051 (m-10) REVERT: N 62 MET cc_start: 0.9353 (mmp) cc_final: 0.8972 (mmm) REVERT: N 71 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8953 (pp20) REVERT: N 105 GLU cc_start: 0.9515 (tp30) cc_final: 0.9266 (tp30) REVERT: O 59 GLU cc_start: 0.9354 (tp30) cc_final: 0.8985 (pm20) REVERT: O 80 THR cc_start: 0.9392 (p) cc_final: 0.8879 (t) REVERT: O 81 ASP cc_start: 0.9307 (m-30) cc_final: 0.9061 (m-30) REVERT: O 90 MET cc_start: 0.9697 (mmp) cc_final: 0.9478 (mmm) REVERT: O 105 GLU cc_start: 0.9129 (mp0) cc_final: 0.8886 (mp0) REVERT: O 106 ASP cc_start: 0.9306 (m-30) cc_final: 0.8975 (m-30) REVERT: P 74 GLU cc_start: 0.9390 (pp20) cc_final: 0.9183 (pp20) REVERT: Q 56 GLU cc_start: 0.9134 (tt0) cc_final: 0.8186 (mt-10) REVERT: R 95 GLN cc_start: 0.9661 (pt0) cc_final: 0.9353 (pp30) REVERT: R 113 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9317 (mm-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0925 time to fit residues: 13.0024 Evaluate side-chains 63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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: 7.9990 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 84 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 = 0.2861 r_free = 0.2861 target = 0.025316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.020480 restraints weight = 241509.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.021127 restraints weight = 113278.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.021576 restraints weight = 67918.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.021881 restraints weight = 46504.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.022076 restraints weight = 35189.202| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2257 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= 0.208 Angle : 0.709 8.861 21563 Z= 0.414 Chirality : 0.046 0.332 2456 Planarity : 0.005 0.061 1498 Dihedral : 33.978 179.093 4789 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.59 (0.28), residues: 825 helix: 1.58 (0.21), residues: 586 sheet: -3.37 (1.39), residues: 10 loop : 0.03 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 116 TYR 0.013 0.002 TYR R 121 PHE 0.015 0.002 PHE R 65 HIS 0.005 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.21 (14846) covalent geometry : angle 0.70924 / 0.41 (21563) hydrogen bonds : bond 0.07583 / 5.03 ( 892) hydrogen bonds : angle 3.92479 / 2.89 ( 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 93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.369 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: 0.9366 (tp30) cc_final: 0.9082 (tp30) REVERT: K 104 PHE cc_start: 0.9607 (m-80) cc_final: 0.9160 (m-80) REVERT: K 120 MET cc_start: 0.8617 (tpp) cc_final: 0.8265 (tpp) REVERT: L 63 GLU cc_start: 0.9605 (pm20) cc_final: 0.9396 (pm20) REVERT: N 37 TYR cc_start: 0.9408 (m-10) cc_final: 0.9067 (m-10) REVERT: N 62 MET cc_start: 0.9350 (mmp) cc_final: 0.8966 (mmm) REVERT: N 71 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8959 (pp20) REVERT: N 102 LEU cc_start: 0.9098 (tp) cc_final: 0.8740 (tp) REVERT: N 105 GLU cc_start: 0.9531 (tp30) cc_final: 0.9262 (tp30) REVERT: O 59 GLU cc_start: 0.9361 (tp30) cc_final: 0.8979 (pm20) REVERT: O 80 THR cc_start: 0.9395 (p) cc_final: 0.8885 (t) REVERT: O 81 ASP cc_start: 0.9325 (m-30) cc_final: 0.9088 (m-30) REVERT: O 104 PHE cc_start: 0.9521 (m-10) cc_final: 0.9170 (m-80) REVERT: O 106 ASP cc_start: 0.9324 (m-30) cc_final: 0.9111 (m-30) REVERT: P 74 GLU cc_start: 0.9376 (pp20) cc_final: 0.9112 (pp20) REVERT: Q 56 GLU cc_start: 0.9086 (tt0) cc_final: 0.8643 (tt0) REVERT: R 95 GLN cc_start: 0.9673 (pt0) cc_final: 0.9366 (pp30) REVERT: R 102 LEU cc_start: 0.9481 (mm) cc_final: 0.9113 (mp) REVERT: R 113 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9313 (mm-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0948 time to fit residues: 13.4826 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 : 0.304 ------------------------------------------------------------------------------- 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: 5.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 90 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 41 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 84 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 = 0.2903 r_free = 0.2903 target = 0.026452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.021508 restraints weight = 237339.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.022156 restraints weight = 110218.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.022687 restraints weight = 65043.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.022986 restraints weight = 42778.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.023169 restraints weight = 33177.554| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14846 Z= 0.147 Angle : 0.684 10.233 21563 Z= 0.397 Chirality : 0.045 0.340 2456 Planarity : 0.004 0.059 1498 Dihedral : 33.780 178.438 4789 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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 (0.29), residues: 825 helix: 1.72 (0.21), residues: 586 sheet: -3.45 (1.19), residues: 10 loop : -0.08 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 42 TYR 0.012 0.001 TYR P 72 PHE 0.016 0.002 PHE O 78 HIS 0.004 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.15 (14846) covalent geometry : angle 0.68354 / 0.40 (21563) hydrogen bonds : bond 0.04618 / 3.03 ( 892) hydrogen bonds : angle 3.63289 / 2.68 ( 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 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.228 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: 0.9385 (tp30) cc_final: 0.9036 (tp30) REVERT: K 104 PHE cc_start: 0.9544 (m-80) cc_final: 0.9045 (m-80) REVERT: K 105 GLU cc_start: 0.9112 (mp0) cc_final: 0.8842 (mp0) REVERT: K 120 MET cc_start: 0.8580 (tpp) cc_final: 0.8228 (tpp) REVERT: L 63 GLU cc_start: 0.9575 (pm20) cc_final: 0.9348 (pm20) REVERT: N 37 TYR cc_start: 0.9377 (m-10) cc_final: 0.9031 (m-10) REVERT: N 62 MET cc_start: 0.9330 (mmp) cc_final: 0.8963 (mmm) REVERT: N 71 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8962 (pp20) REVERT: N 102 LEU cc_start: 0.9049 (tp) cc_final: 0.8691 (tp) REVERT: N 105 GLU cc_start: 0.9565 (tp30) cc_final: 0.9312 (tp30) REVERT: O 59 GLU cc_start: 0.9400 (tp30) cc_final: 0.9074 (pm20) REVERT: O 80 THR cc_start: 0.9435 (p) cc_final: 0.8907 (t) REVERT: O 81 ASP cc_start: 0.9359 (m-30) cc_final: 0.9115 (m-30) REVERT: O 104 PHE cc_start: 0.9453 (m-10) cc_final: 0.9098 (m-80) REVERT: P 74 GLU cc_start: 0.9307 (pp20) cc_final: 0.9028 (pp20) REVERT: Q 56 GLU cc_start: 0.9008 (tt0) cc_final: 0.8565 (tt0) REVERT: Q 61 GLU cc_start: 0.9404 (pp20) cc_final: 0.9076 (pp20) REVERT: Q 64 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9248 (mm-30) REVERT: Q 95 LYS cc_start: 0.8887 (pptt) cc_final: 0.7924 (tptt) REVERT: R 113 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9319 (mm-30) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0962 time to fit residues: 15.1401 Evaluate side-chains 76 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 30.0000 chunk 48 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 50.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 84 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 = 0.2897 r_free = 0.2897 target = 0.026272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.021336 restraints weight = 236435.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.021989 restraints weight = 111616.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.022498 restraints weight = 66000.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.022804 restraints weight = 45034.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.023022 restraints weight = 33610.016| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14846 Z= 0.153 Angle : 0.674 7.160 21563 Z= 0.392 Chirality : 0.045 0.331 2456 Planarity : 0.004 0.063 1498 Dihedral : 33.688 178.819 4789 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.79 (0.29), residues: 825 helix: 1.78 (0.21), residues: 584 sheet: -3.61 (1.16), residues: 10 loop : -0.01 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 63 TYR 0.012 0.001 TYR N 37 PHE 0.017 0.002 PHE R 65 HIS 0.004 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.15 (14846) covalent geometry : angle 0.67374 / 0.39 (21563) hydrogen bonds : bond 0.05422 / 3.58 ( 892) hydrogen bonds : angle 3.66361 / 2.71 ( 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 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.249 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: 0.9410 (tp30) cc_final: 0.9102 (tp30) REVERT: K 104 PHE cc_start: 0.9557 (m-80) cc_final: 0.9085 (m-80) REVERT: K 120 MET cc_start: 0.8596 (tpp) cc_final: 0.8252 (tpp) REVERT: L 63 GLU cc_start: 0.9576 (pm20) cc_final: 0.9352 (pm20) REVERT: N 59 MET cc_start: 0.9165 (tpp) cc_final: 0.8952 (tpt) REVERT: N 62 MET cc_start: 0.9364 (mmp) cc_final: 0.8955 (mmm) REVERT: N 71 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8968 (pp20) REVERT: N 102 LEU cc_start: 0.9005 (tp) cc_final: 0.8628 (tp) REVERT: N 105 GLU cc_start: 0.9564 (tp30) cc_final: 0.9329 (tp30) REVERT: O 59 GLU cc_start: 0.9443 (tp30) cc_final: 0.9084 (pm20) REVERT: O 78 PHE cc_start: 0.9094 (t80) cc_final: 0.8869 (t80) REVERT: O 80 THR cc_start: 0.9450 (p) cc_final: 0.8923 (t) REVERT: O 81 ASP cc_start: 0.9355 (m-30) cc_final: 0.9114 (m-30) REVERT: O 104 PHE cc_start: 0.9443 (m-10) cc_final: 0.9109 (m-80) REVERT: O 106 ASP cc_start: 0.9357 (m-30) cc_final: 0.9106 (m-30) REVERT: P 74 GLU cc_start: 0.9358 (pp20) cc_final: 0.9091 (pp20) REVERT: Q 56 GLU cc_start: 0.9047 (tt0) cc_final: 0.8605 (tt0) REVERT: Q 64 GLU cc_start: 0.9612 (mm-30) cc_final: 0.9234 (mm-30) REVERT: Q 95 LYS cc_start: 0.8915 (pptt) cc_final: 0.7950 (tptt) REVERT: R 109 HIS cc_start: 0.9593 (m90) cc_final: 0.9285 (m90) REVERT: R 113 GLU cc_start: 0.9626 (mm-30) cc_final: 0.9333 (mm-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1003 time to fit residues: 15.0498 Evaluate side-chains 75 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 8.9990 chunk 81 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.024610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.019935 restraints weight = 250184.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.020534 restraints weight = 118847.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.021000 restraints weight = 70680.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.021290 restraints weight = 48922.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.021459 restraints weight = 36810.545| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14846 Z= 0.266 Angle : 0.774 10.623 21563 Z= 0.442 Chirality : 0.048 0.328 2456 Planarity : 0.006 0.065 1498 Dihedral : 33.936 179.271 4789 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 1.34 (0.28), residues: 825 helix: 1.42 (0.21), residues: 584 sheet: -3.53 (1.22), residues: 10 loop : -0.12 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 77 TYR 0.017 0.002 TYR R 40 PHE 0.012 0.002 PHE L 100 HIS 0.007 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.27 (14846) covalent geometry : angle 0.77359 / 0.44 (21563) hydrogen bonds : bond 0.11253 / 7.49 ( 892) hydrogen bonds : angle 4.12948 / 3.06 ( 2205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.50 seconds wall clock time: 28 minutes 2.67 seconds (1682.67 seconds total)