Starting phenix.real_space_refine on Sat Oct 24 19:04:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf4_13367/10_2026/7pf4_13367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf4_13367/10_2026/7pf4_13367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pf4_13367/10_2026/7pf4_13367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf4_13367/10_2026/7pf4_13367.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf4_13367/10_2026/7pf4_13367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf4_13367/10_2026/7pf4_13367.cif" } resolution = 4.0 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= -0.000 sd= 0.003 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 334 5.49 5 S 10 5.16 5 C 7084 2.51 5 N 2431 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12935 Number of models: 1 Model: "" Number of chains: 10 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: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Time building chain proxies: 2.79, per 1000 atoms: 0.22 Number of scatterers: 12935 At special positions: 0 Unit cell: (116.55, 152.25, 117.6, 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 334 15.00 O 3076 8.00 N 2431 7.00 C 7084 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: 1.04 Conformation dependent library (CDL) restraints added in 505.0 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 71.1% alpha, 2.1% beta 165 base pairs and 285 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.711A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.781A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 3.992A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.207A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 36 removed outlier: 3.668A pdb=" N VAL M 30 " --> pdb=" O PRO M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.053A 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 removed outlier: 3.550A pdb=" N VAL N 41 " --> pdb=" O TYR N 37 " (cutoff:3.500A) 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 79 removed outlier: 3.764A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 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: 3.759A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 36 removed outlier: 3.669A pdb=" N VAL Q 30 " --> pdb=" O PRO Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.285A 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 '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 123 removed outlier: 3.695A pdb=" N ALA R 107 " --> pdb=" O PRO R 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.735A 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 'M' and resid 42 through 43 removed outlier: 7.229A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.675A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.181A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'Q' and resid 77 through 78 399 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 165 basepair parallelities 285 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2644 1.34 - 1.46: 4652 1.46 - 1.58: 5866 1.58 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 13848 Sorted by residual: bond pdb=" C5' DA I 453 " pdb=" C4' DA I 453 " ideal model delta sigma weight residual 1.512 1.542 -0.030 7.00e-03 2.04e+04 1.79e+01 bond pdb=" C3' DG I 522 " pdb=" O3' DG I 522 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C5' DA I 433 " pdb=" C4' DA I 433 " ideal model delta sigma weight residual 1.512 1.538 -0.026 7.00e-03 2.04e+04 1.33e+01 bond pdb=" C3' DG I 410 " pdb=" O3' DG I 410 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C5' DA I 525 " pdb=" C4' DA I 525 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.14e+01 ... (remaining 13843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 19531 2.52 - 5.03: 543 5.03 - 7.55: 49 7.55 - 10.06: 10 10.06 - 12.58: 2 Bond angle restraints: 20135 Sorted by residual: angle pdb=" CA GLU K 97 " pdb=" CB GLU K 97 " pdb=" CG GLU K 97 " ideal model delta sigma weight residual 114.10 126.68 -12.58 2.00e+00 2.50e-01 3.95e+01 angle pdb=" C ILE M 87 " pdb=" N ARG M 88 " pdb=" CA ARG M 88 " ideal model delta sigma weight residual 122.73 112.87 9.86 1.61e+00 3.86e-01 3.75e+01 angle pdb=" O4' DG J 308 " pdb=" C1' DG J 308 " pdb=" N9 DG J 308 " ideal model delta sigma weight residual 108.00 112.01 -4.01 7.00e-01 2.04e+00 3.29e+01 angle pdb=" O4' DG J 354 " pdb=" C1' DG J 354 " pdb=" N9 DG J 354 " ideal model delta sigma weight residual 108.00 112.01 -4.01 7.00e-01 2.04e+00 3.28e+01 angle pdb=" O4' DT J 295 " pdb=" C4' DT J 295 " pdb=" C3' DT J 295 " ideal model delta sigma weight residual 106.00 102.57 3.43 6.00e-01 2.78e+00 3.27e+01 ... (remaining 20130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 5688 35.22 - 70.44: 1736 70.44 - 105.66: 33 105.66 - 140.88: 2 140.88 - 176.09: 1 Dihedral angle restraints: 7460 sinusoidal: 5238 harmonic: 2222 Sorted by residual: dihedral pdb=" CA ARG L 23 " pdb=" C ARG L 23 " pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta harmonic sigma weight residual -180.00 -149.36 -30.64 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA ARG M 88 " pdb=" C ARG M 88 " pdb=" N ASN M 89 " pdb=" CA ASN M 89 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PRO M 26 " pdb=" C PRO M 26 " pdb=" N VAL M 27 " pdb=" CA VAL M 27 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 7457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1662 0.051 - 0.102: 522 0.102 - 0.153: 78 0.153 - 0.205: 19 0.205 - 0.256: 7 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA GLU K 97 " pdb=" N GLU K 97 " pdb=" C GLU K 97 " pdb=" CB GLU K 97 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PHE K 104 " pdb=" N PHE K 104 " pdb=" C PHE K 104 " pdb=" CB PHE K 104 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU N 45 " pdb=" CB LEU N 45 " pdb=" CD1 LEU N 45 " pdb=" CD2 LEU N 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2285 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE M 25 " 0.065 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO M 26 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO M 26 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 26 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " -0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO M 80 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 85 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LYS N 85 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS N 85 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG N 86 " 0.016 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2610 2.79 - 3.31: 11699 3.31 - 3.84: 27751 3.84 - 4.37: 30869 4.37 - 4.90: 42548 Nonbonded interactions: 115477 Sorted by model distance: nonbonded pdb=" O THR M 76 " pdb=" OG1 THR N 52 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG L 78 " pdb=" O THR L 80 " model vdw 2.325 3.120 nonbonded pdb=" N GLY Q 44 " pdb=" O ILE R 89 " model vdw 2.335 3.120 nonbonded pdb=" OH TYR Q 39 " pdb=" OE1 GLU R 71 " model vdw 2.336 3.040 nonbonded pdb=" N GLY M 44 " pdb=" O ILE N 89 " model vdw 2.336 3.120 ... (remaining 115472 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: 2.590 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 0.053 13848 Z= 0.578 Angle : 1.029 12.577 20135 Z= 0.829 Chirality : 0.051 0.256 2288 Planarity : 0.007 0.100 1390 Dihedral : 29.722 176.094 6028 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.80 (0.27), residues: 752 helix: -0.21 (0.20), residues: 534 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 45 TYR 0.038 0.003 TYR O 99 PHE 0.021 0.003 PHE N 65 HIS 0.008 0.002 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.58 (13848) covalent geometry : angle 1.02934 / 0.83 (20135) hydrogen bonds : bond 0.09572 / 6.31 ( 822) hydrogen bonds : angle 4.76338 / 3.34 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8532 (mm-30) REVERT: K 96 SER cc_start: 0.9070 (m) cc_final: 0.8859 (p) REVERT: K 99 TYR cc_start: 0.8859 (t80) cc_final: 0.8502 (t80) REVERT: K 106 ASP cc_start: 0.8751 (m-30) cc_final: 0.8529 (m-30) REVERT: L 49 LEU cc_start: 0.8979 (mp) cc_final: 0.8723 (mp) REVERT: M 25 PHE cc_start: 0.7803 (m-80) cc_final: 0.7570 (m-10) REVERT: N 52 THR cc_start: 0.8016 (t) cc_final: 0.7471 (t) REVERT: N 71 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8272 (tt0) REVERT: N 95 GLN cc_start: 0.8630 (pp30) cc_final: 0.8074 (tm-30) REVERT: N 105 GLU cc_start: 0.7939 (tp30) cc_final: 0.7627 (tp30) REVERT: N 108 LYS cc_start: 0.9269 (ptmm) cc_final: 0.8529 (ptmm) REVERT: N 116 LYS cc_start: 0.9457 (tmmt) cc_final: 0.8431 (tmtt) REVERT: O 97 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8055 (mt-10) REVERT: Q 79 ILE cc_start: 0.8482 (mm) cc_final: 0.7912 (pt) REVERT: R 51 ASP cc_start: 0.8340 (p0) cc_final: 0.8092 (p0) REVERT: R 95 GLN cc_start: 0.8624 (tm130) cc_final: 0.8363 (tm-30) REVERT: R 102 LEU cc_start: 0.9333 (mt) cc_final: 0.9091 (mp) REVERT: R 105 GLU cc_start: 0.8324 (mp0) cc_final: 0.7884 (mp0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1148 time to fit residues: 27.7322 Evaluate side-chains 118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN O 93 GLN R 47 GLN R 82 HIS ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.063789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.052002 restraints weight = 118369.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.053156 restraints weight = 68607.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.053812 restraints weight = 47254.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.054326 restraints weight = 37719.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.054696 restraints weight = 31671.635| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13848 Z= 0.168 Angle : 0.772 10.769 20135 Z= 0.444 Chirality : 0.050 0.268 2288 Planarity : 0.006 0.066 1390 Dihedral : 32.872 179.561 4504 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.26 % Allowed : 9.75 % Favored : 88.99 % 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: 0.17 (0.28), residues: 752 helix: 0.54 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 45 TYR 0.028 0.002 TYR P 88 PHE 0.012 0.002 PHE P 61 HIS 0.010 0.002 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.17 (13848) covalent geometry : angle 0.77194 / 0.44 (20135) hydrogen bonds : bond 0.05305 / 3.58 ( 822) hydrogen bonds : angle 3.72418 / 2.62 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 LYS cc_start: 0.8762 (tppt) cc_final: 0.8532 (tptp) REVERT: K 100 LEU cc_start: 0.9260 (mt) cc_final: 0.8616 (mm) REVERT: K 104 PHE cc_start: 0.9229 (m-10) cc_final: 0.8730 (m-80) REVERT: K 105 GLU cc_start: 0.8806 (mp0) cc_final: 0.8542 (mp0) REVERT: L 59 LYS cc_start: 0.8989 (tppt) cc_final: 0.8733 (tppp) REVERT: N 85 LYS cc_start: 0.9294 (ttpt) cc_final: 0.8962 (ttpp) REVERT: N 91 SER cc_start: 0.8493 (p) cc_final: 0.8140 (p) REVERT: N 95 GLN cc_start: 0.8488 (pp30) cc_final: 0.7874 (tm-30) REVERT: N 99 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8417 (mtt90) REVERT: N 105 GLU cc_start: 0.7999 (tp30) cc_final: 0.7792 (tp30) REVERT: N 108 LYS cc_start: 0.9353 (ptmm) cc_final: 0.8611 (ptmm) REVERT: O 59 GLU cc_start: 0.8522 (pm20) cc_final: 0.8309 (pm20) REVERT: O 97 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8194 (mt-10) REVERT: R 51 ASP cc_start: 0.8119 (p0) cc_final: 0.7892 (p0) REVERT: R 108 LYS cc_start: 0.9399 (mtmt) cc_final: 0.9179 (mtmm) outliers start: 8 outliers final: 4 residues processed: 144 average time/residue: 0.1131 time to fit residues: 23.2476 Evaluate side-chains 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [60, 52, 55, 43, 66, 93, 17, 63, 97, 9, 81] chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 0.0270 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 9 optimal weight: 0.0370 chunk 81 optimal weight: 20.0000 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.063859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.052098 restraints weight = 118631.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.053255 restraints weight = 68596.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.053944 restraints weight = 47062.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.054473 restraints weight = 37177.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.054769 restraints weight = 31154.319| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 13848 Z= 0.149 Angle : 0.717 10.002 20135 Z= 0.411 Chirality : 0.048 0.263 2288 Planarity : 0.005 0.065 1390 Dihedral : 32.786 175.307 4504 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.57 % Allowed : 10.85 % Favored : 87.58 % 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: 0.60 (0.29), residues: 752 helix: 0.93 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 40 TYR 0.032 0.002 TYR P 88 PHE 0.014 0.002 PHE O 67 HIS 0.008 0.001 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.15 (13848) covalent geometry : angle 0.71705 / 0.41 (20135) hydrogen bonds : bond 0.04609 / 3.08 ( 822) hydrogen bonds : angle 3.44162 / 2.43 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.315 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: 0.9152 (m-10) cc_final: 0.8634 (m-80) REVERT: K 105 GLU cc_start: 0.8706 (mp0) cc_final: 0.8458 (mp0) REVERT: K 125 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: L 59 LYS cc_start: 0.9012 (tppt) cc_final: 0.8790 (tppp) REVERT: N 91 SER cc_start: 0.8434 (p) cc_final: 0.8173 (p) REVERT: N 95 GLN cc_start: 0.8536 (pp30) cc_final: 0.7348 (tm-30) REVERT: N 99 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8331 (mtm-85) REVERT: N 108 LYS cc_start: 0.9352 (ptmm) cc_final: 0.8996 (ptmm) REVERT: N 120 LYS cc_start: 0.9346 (mmtp) cc_final: 0.9075 (mmtm) REVERT: P 79 LYS cc_start: 0.8164 (tppt) cc_final: 0.7709 (tppt) REVERT: R 51 ASP cc_start: 0.8136 (p0) cc_final: 0.7904 (p0) REVERT: R 108 LYS cc_start: 0.9398 (mtmt) cc_final: 0.9163 (mtmm) outliers start: 10 outliers final: 3 residues processed: 137 average time/residue: 0.1078 time to fit residues: 21.6926 Evaluate side-chains 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain R residue 42 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [69, 35, 14, 22, 99, 73, 4, 31, 87, 45, 52] chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.061452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.049619 restraints weight = 120705.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050757 restraints weight = 70137.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.051451 restraints weight = 48445.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.051876 restraints weight = 37971.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.052184 restraints weight = 32715.244| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13848 Z= 0.205 Angle : 0.742 12.622 20135 Z= 0.419 Chirality : 0.047 0.368 2288 Planarity : 0.005 0.066 1390 Dihedral : 32.826 174.723 4504 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.36 % Allowed : 13.52 % Favored : 84.12 % 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: 0.86 (0.29), residues: 752 helix: 1.13 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.81 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 99 TYR 0.052 0.003 TYR R 83 PHE 0.025 0.003 PHE O 104 HIS 0.008 0.001 HIS N 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.21 (13848) covalent geometry : angle 0.74171 / 0.42 (20135) hydrogen bonds : bond 0.06621 / 4.49 ( 822) hydrogen bonds : angle 3.54057 / 2.52 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 105 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8577 (mp0) REVERT: L 59 LYS cc_start: 0.9059 (tppt) cc_final: 0.8845 (tppp) REVERT: N 85 LYS cc_start: 0.9375 (ttpt) cc_final: 0.8989 (ttpp) REVERT: N 95 GLN cc_start: 0.8630 (pp30) cc_final: 0.8130 (tm-30) REVERT: O 54 TYR cc_start: 0.8616 (m-80) cc_final: 0.8272 (m-80) REVERT: O 97 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7883 (mt-10) REVERT: R 108 LYS cc_start: 0.9432 (mtmt) cc_final: 0.9197 (mtmm) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 0.1104 time to fit residues: 20.0650 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [25, 18, 7, 1, 34, 45, 8, 3, 58, 54, 39] chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.0010 chunk 3 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 HIS O 55 GLN ** Q 84 GLN ** 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 = 0.3853 r_free = 0.3853 target = 0.062681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.050769 restraints weight = 119556.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.051880 restraints weight = 68924.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.052633 restraints weight = 48152.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.053055 restraints weight = 37357.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.053396 restraints weight = 32083.906| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13848 Z= 0.150 Angle : 0.708 13.543 20135 Z= 0.403 Chirality : 0.046 0.363 2288 Planarity : 0.005 0.065 1390 Dihedral : 32.803 173.823 4504 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.20 % Allowed : 15.88 % Favored : 81.92 % 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: 0.95 (0.30), residues: 752 helix: 1.20 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.80 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 79 TYR 0.034 0.002 TYR P 88 PHE 0.026 0.003 PHE O 104 HIS 0.011 0.001 HIS N 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (13848) covalent geometry : angle 0.70827 / 0.40 (20135) hydrogen bonds : bond 0.04617 / 3.09 ( 822) hydrogen bonds : angle 3.44764 / 2.43 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 105 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8359 (mp0) REVERT: L 59 LYS cc_start: 0.9071 (tppt) cc_final: 0.8760 (tppp) REVERT: N 95 GLN cc_start: 0.8595 (pp30) cc_final: 0.8041 (tm-30) REVERT: N 105 GLU cc_start: 0.8003 (tp30) cc_final: 0.7752 (tp30) REVERT: O 54 TYR cc_start: 0.8537 (m-80) cc_final: 0.8233 (m-80) REVERT: R 108 LYS cc_start: 0.9390 (mtmt) cc_final: 0.9138 (mtmm) outliers start: 14 outliers final: 12 residues processed: 126 average time/residue: 0.1051 time to fit residues: 19.7330 Evaluate side-chains 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [68, 55, 39, 97, 56, 21, 74, 46, 31, 61, 43] chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.062315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.050489 restraints weight = 119230.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051626 restraints weight = 68410.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.052329 restraints weight = 47110.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.052833 restraints weight = 36885.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.053115 restraints weight = 31218.179| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13848 Z= 0.153 Angle : 0.709 13.701 20135 Z= 0.401 Chirality : 0.045 0.276 2288 Planarity : 0.005 0.064 1390 Dihedral : 32.721 173.329 4504 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.20 % Allowed : 17.30 % Favored : 80.50 % 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: 0.95 (0.30), residues: 752 helix: 1.19 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 79 TYR 0.028 0.002 TYR M 57 PHE 0.030 0.003 PHE O 104 HIS 0.003 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (13848) covalent geometry : angle 0.70858 / 0.40 (20135) hydrogen bonds : bond 0.04934 / 3.31 ( 822) hydrogen bonds : angle 3.40640 / 2.41 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9060 (m-10) cc_final: 0.8839 (m-10) REVERT: K 105 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8333 (mp0) REVERT: N 85 LYS cc_start: 0.9384 (ttpt) cc_final: 0.9123 (ttpt) REVERT: N 95 GLN cc_start: 0.8649 (pp30) cc_final: 0.8300 (pp30) REVERT: O 54 TYR cc_start: 0.8550 (m-80) cc_final: 0.8256 (m-80) REVERT: R 108 LYS cc_start: 0.9396 (mtmt) cc_final: 0.9154 (mtmm) outliers start: 14 outliers final: 13 residues processed: 124 average time/residue: 0.1028 time to fit residues: 19.0257 Evaluate side-chains 118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [28, 83, 21, 80, 10, 35, 59, 84, 52, 76, 41] chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.061931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.050091 restraints weight = 119905.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.051218 restraints weight = 68986.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.051915 restraints weight = 47653.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.052418 restraints weight = 37421.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.052765 restraints weight = 31589.800| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13848 Z= 0.167 Angle : 0.707 13.711 20135 Z= 0.400 Chirality : 0.045 0.272 2288 Planarity : 0.005 0.064 1390 Dihedral : 32.710 173.125 4504 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.04 % Allowed : 18.87 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.30), residues: 752 helix: 1.13 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.74 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.018 0.002 TYR M 57 PHE 0.032 0.003 PHE O 104 HIS 0.003 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (13848) covalent geometry : angle 0.70693 / 0.40 (20135) hydrogen bonds : bond 0.05217 / 3.51 ( 822) hydrogen bonds : angle 3.47103 / 2.46 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9094 (m-10) cc_final: 0.8798 (m-10) REVERT: K 105 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8331 (mp0) REVERT: N 85 LYS cc_start: 0.9401 (ttpt) cc_final: 0.9138 (ttpt) REVERT: N 95 GLN cc_start: 0.8685 (pp30) cc_final: 0.8329 (pp30) REVERT: N 109 HIS cc_start: 0.9113 (m170) cc_final: 0.8590 (m170) REVERT: N 120 LYS cc_start: 0.9395 (mmtp) cc_final: 0.9160 (mmtm) REVERT: O 54 TYR cc_start: 0.8584 (m-80) cc_final: 0.8326 (m-80) REVERT: R 108 LYS cc_start: 0.9390 (mtmt) cc_final: 0.9140 (mtmm) outliers start: 13 outliers final: 12 residues processed: 114 average time/residue: 0.0987 time to fit residues: 17.0638 Evaluate side-chains 115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [47, 13, 23, 88, 53, 3, 39, 26, 74, 56, 35] chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.0020 chunk 88 optimal weight: 50.0000 chunk 53 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN O 108 ASN ** Q 84 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.062281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.050484 restraints weight = 118021.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051596 restraints weight = 68097.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.052300 restraints weight = 47096.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.052751 restraints weight = 36914.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.053072 restraints weight = 31528.856| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13848 Z= 0.150 Angle : 0.696 14.393 20135 Z= 0.394 Chirality : 0.044 0.279 2288 Planarity : 0.005 0.064 1390 Dihedral : 32.679 173.061 4504 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.52 % Allowed : 19.50 % Favored : 77.99 % 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: 0.95 (0.30), residues: 752 helix: 1.17 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 86 TYR 0.023 0.002 TYR M 57 PHE 0.030 0.002 PHE P 61 HIS 0.002 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (13848) covalent geometry : angle 0.69647 / 0.39 (20135) hydrogen bonds : bond 0.04688 / 3.14 ( 822) hydrogen bonds : angle 3.40227 / 2.41 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.281 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: 0.9120 (m-10) cc_final: 0.8797 (m-10) REVERT: K 105 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8456 (mp0) REVERT: N 85 LYS cc_start: 0.9415 (ttpt) cc_final: 0.9151 (ttpt) REVERT: N 95 GLN cc_start: 0.8698 (pp30) cc_final: 0.8324 (pp30) REVERT: N 120 LYS cc_start: 0.9360 (mmtp) cc_final: 0.9141 (mmtm) REVERT: O 54 TYR cc_start: 0.8584 (m-80) cc_final: 0.8283 (m-80) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.0991 time to fit residues: 18.5866 Evaluate side-chains 119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [54, 15, 17, 50, 5, 12, 83, 30, 46, 58, 103] chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.060623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048889 restraints weight = 121554.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.049980 restraints weight = 69591.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050715 restraints weight = 48140.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.051173 restraints weight = 37659.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.051464 restraints weight = 31980.224| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13848 Z= 0.199 Angle : 0.741 12.813 20135 Z= 0.415 Chirality : 0.045 0.311 2288 Planarity : 0.005 0.065 1390 Dihedral : 32.738 173.621 4504 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.20 % Allowed : 21.54 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 752 helix: 1.01 (0.21), residues: 552 sheet: None (None), residues: 0 loop : -0.67 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 78 TYR 0.018 0.002 TYR M 57 PHE 0.039 0.003 PHE P 61 HIS 0.007 0.001 HIS R 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (13848) covalent geometry : angle 0.74146 / 0.42 (20135) hydrogen bonds : bond 0.06480 / 4.40 ( 822) hydrogen bonds : angle 3.57639 / 2.54 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9112 (m-10) cc_final: 0.8831 (m-10) REVERT: K 105 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8446 (mp0) REVERT: N 85 LYS cc_start: 0.9411 (ttpt) cc_final: 0.9155 (ttpt) REVERT: N 95 GLN cc_start: 0.8740 (pp30) cc_final: 0.8352 (pp30) REVERT: O 54 TYR cc_start: 0.8613 (m-80) cc_final: 0.8353 (m-80) REVERT: R 108 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9223 (mtmm) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.1013 time to fit residues: 17.8554 Evaluate side-chains 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [47, 24, 5, 93, 39, 38, 22, 96, 23, 58, 70] chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.061958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.050128 restraints weight = 119493.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.051267 restraints weight = 68631.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.051985 restraints weight = 47273.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.052484 restraints weight = 36829.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.052871 restraints weight = 31069.393| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13848 Z= 0.150 Angle : 0.729 15.138 20135 Z= 0.408 Chirality : 0.045 0.289 2288 Planarity : 0.005 0.063 1390 Dihedral : 32.728 173.351 4504 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.57 % Allowed : 22.80 % Favored : 75.63 % 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: 0.90 (0.30), residues: 752 helix: 1.11 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.67 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 42 TYR 0.018 0.002 TYR M 57 PHE 0.037 0.002 PHE P 61 HIS 0.005 0.001 HIS N 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (13848) covalent geometry : angle 0.72948 / 0.41 (20135) hydrogen bonds : bond 0.04549 / 3.03 ( 822) hydrogen bonds : angle 3.48117 / 2.47 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.300 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: 0.9102 (m-10) cc_final: 0.8794 (m-10) REVERT: K 105 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8439 (mp0) REVERT: N 85 LYS cc_start: 0.9398 (ttpt) cc_final: 0.9150 (ttpt) REVERT: N 95 GLN cc_start: 0.8700 (pp30) cc_final: 0.8309 (pp30) REVERT: O 54 TYR cc_start: 0.8564 (m-80) cc_final: 0.8271 (m-80) REVERT: R 105 GLU cc_start: 0.8020 (mp0) cc_final: 0.7643 (mp0) REVERT: R 108 LYS cc_start: 0.9438 (mtmt) cc_final: 0.9220 (mtmm) outliers start: 10 outliers final: 10 residues processed: 114 average time/residue: 0.0991 time to fit residues: 16.9833 Evaluate side-chains 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [85, 44, 45, 18, 48, 74, 8, 6, 9, 58, 47] chunk 85 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 0.0030 chunk 48 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.061509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.049760 restraints weight = 119408.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050883 restraints weight = 68265.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.051577 restraints weight = 47122.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.052077 restraints weight = 36925.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.052375 restraints weight = 31163.186| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13848 Z= 0.158 Angle : 0.711 14.297 20135 Z= 0.400 Chirality : 0.044 0.275 2288 Planarity : 0.005 0.063 1390 Dihedral : 32.627 172.603 4504 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 22.33 % Favored : 75.79 % 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: 0.96 (0.30), residues: 752 helix: 1.12 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.58 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.016 0.002 TYR P 88 PHE 0.024 0.002 PHE P 61 HIS 0.003 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13848) covalent geometry : angle 0.71118 / 0.40 (20135) hydrogen bonds : bond 0.05081 / 3.42 ( 822) hydrogen bonds : angle 3.42688 / 2.43 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.71 seconds wall clock time: 36 minutes 23.29 seconds (2183.29 seconds total)