Starting phenix.real_space_refine on Sat Sep 12 09:43:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf5_13368/09_2026/7pf5_13368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf5_13368/09_2026/7pf5_13368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pf5_13368/09_2026/7pf5_13368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf5_13368/09_2026/7pf5_13368.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf5_13368/09_2026/7pf5_13368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf5_13368/09_2026/7pf5_13368.cif" } resolution = 3.8 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= 0.008 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 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "a" 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: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "g" 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: "h" 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} Chain: "u" 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: 2.84, per 1000 atoms: 0.21 Number of scatterers: 13470 At special positions: 0 Unit cell: (99.75, 133.35, 126, 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 3178 8.00 N 2528 7.00 C 7420 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: 1.22 Conformation dependent library (CDL) restraints added in 450.6 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: 36 helices and 9 sheets defined 69.6% alpha, 2.6% beta 165 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.568A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.549A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 77 removed outlier: 4.024A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.247A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.555A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.951A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.572A pdb=" N GLN f 93 " --> pdb=" O ALA f 89 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.020A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 removed outlier: 3.507A pdb=" N ASN g 89 " --> pdb=" O LEU g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.711A pdb=" N VAL h 41 " --> pdb=" O TYR h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.528A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 124 removed outlier: 3.677A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 51 removed outlier: 3.991A pdb=" N LEU u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER u 50 " --> pdb=" O ALA u 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS u 51 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 69 Processing helix chain 'u' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.871A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 118 through 119 removed outlier: 3.500A pdb=" N ILE a 119 " --> pdb=" O ARG b 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.183A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.925A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.331A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'u' and resid 56 through 57 433 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 165 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 1.67 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: 2457 1.33 - 1.45: 4977 1.45 - 1.58: 6266 1.58 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DT J 522 " pdb=" C2' DT J 522 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.74e+01 bond pdb=" C3' DG J 463 " pdb=" O3' DG J 463 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C3' DG J 541 " pdb=" O3' DG J 541 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" C5' DG I 328 " pdb=" C4' DG I 328 " ideal model delta sigma weight residual 1.512 1.538 -0.026 7.00e-03 2.04e+04 1.38e+01 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19733 2.17 - 4.33: 1022 4.33 - 6.50: 74 6.50 - 8.67: 18 8.67 - 10.84: 6 Bond angle restraints: 20853 Sorted by residual: angle pdb=" O5' DG I 328 " pdb=" C5' DG I 328 " pdb=" C4' DG I 328 " ideal model delta sigma weight residual 109.40 113.58 -4.18 8.00e-01 1.56e+00 2.73e+01 angle pdb=" O4' DA I 348 " pdb=" C4' DA I 348 " pdb=" C3' DA I 348 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.56e+01 angle pdb=" O4' DC J 471 " pdb=" C4' DC J 471 " pdb=" C3' DC J 471 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" O4' DC I 279 " pdb=" C1' DC I 279 " pdb=" N1 DC I 279 " ideal model delta sigma weight residual 108.00 111.49 -3.49 7.00e-01 2.04e+00 2.48e+01 angle pdb=" O4' DT J 409 " pdb=" C4' DT J 409 " pdb=" C3' DT J 409 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6119 35.82 - 71.64: 1652 71.64 - 107.45: 24 107.45 - 143.27: 1 143.27 - 179.09: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA TYR e 54 " pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR d 88 " pdb=" C THR d 88 " pdb=" N ILE d 89 " pdb=" CA ILE d 89 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DG I 335 " pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " pdb=" P DT I 336 " ideal model delta sinusoidal sigma weight residual -140.00 39.09 -179.09 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1573 0.048 - 0.097: 633 0.097 - 0.145: 138 0.145 - 0.193: 23 0.193 - 0.242: 9 Chirality restraints: 2376 Sorted by residual: chirality pdb=" C3' DG I 335 " pdb=" C4' DG I 335 " pdb=" O3' DG I 335 " pdb=" C2' DG I 335 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLN e 55 " pdb=" N GLN e 55 " pdb=" C GLN e 55 " pdb=" CB GLN e 55 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE d 89 " pdb=" CA ILE d 89 " pdb=" CG1 ILE d 89 " pdb=" CG2 ILE d 89 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE e 51 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ILE e 51 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE e 51 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG e 52 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL f 70 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C VAL f 70 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL f 70 " 0.019 2.00e-02 2.50e+03 pdb=" N THR f 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 99 " 0.206 9.50e-02 1.11e+02 9.27e-02 6.37e+00 pdb=" NE ARG d 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG d 99 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG d 99 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG d 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2832 2.79 - 3.32: 12441 3.32 - 3.85: 28918 3.85 - 4.37: 31999 4.37 - 4.90: 44664 Nonbonded interactions: 120854 Sorted by model distance: nonbonded pdb=" O TYR c 39 " pdb=" OG SER d 78 " model vdw 2.264 3.040 nonbonded pdb=" NH2 ARG c 81 " pdb=" O GLN e 55 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG g 29 " pdb=" OE2 GLU h 35 " model vdw 2.295 3.120 nonbonded pdb=" ND2 ASN a 108 " pdb=" O GLY b 42 " model vdw 2.296 3.120 nonbonded pdb=" O THR g 16 " pdb=" OG SER g 19 " model vdw 2.296 3.040 ... (remaining 120849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.500 Find NCS groups from input model: 0.140 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:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.071 14386 Z= 0.605 Angle : 1.023 10.836 20853 Z= 0.795 Chirality : 0.054 0.242 2376 Planarity : 0.007 0.093 1478 Dihedral : 28.940 179.090 6233 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: -0.59 (0.26), residues: 825 helix: -0.07 (0.19), residues: 573 sheet: -0.81 (1.73), residues: 10 loop : -0.85 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG d 99 TYR 0.034 0.004 TYR a 54 PHE 0.043 0.002 PHE e 104 HIS 0.009 0.002 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.60 (14386) covalent geometry : angle 1.02265 / 0.80 (20853) hydrogen bonds : bond 0.09845 / 6.54 ( 856) hydrogen bonds : angle 4.76893 / 3.48 ( 2133) *********************** 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 150 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9120 (m-80) cc_final: 0.8696 (m-80) REVERT: a 79 LYS cc_start: 0.8496 (tmtt) cc_final: 0.8283 (tmtt) REVERT: a 90 MET cc_start: 0.8857 (mpp) cc_final: 0.8634 (mpp) REVERT: b 70 VAL cc_start: 0.9567 (t) cc_final: 0.9284 (t) REVERT: b 85 ASP cc_start: 0.7900 (m-30) cc_final: 0.7677 (m-30) REVERT: c 30 VAL cc_start: 0.8230 (t) cc_final: 0.8020 (t) REVERT: c 36 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8596 (mmmt) REVERT: c 61 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8120 (mt-10) REVERT: d 65 PHE cc_start: 0.8827 (t80) cc_final: 0.8617 (t80) REVERT: f 74 GLU cc_start: 0.8709 (pm20) cc_final: 0.8438 (pm20) REVERT: g 61 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8497 (tm-30) REVERT: g 62 ILE cc_start: 0.9528 (pt) cc_final: 0.9196 (pt) REVERT: g 95 LYS cc_start: 0.8892 (tptt) cc_final: 0.8212 (mmmm) REVERT: h 33 ARG cc_start: 0.6629 (mtp-110) cc_final: 0.6094 (mtt-85) REVERT: h 51 ASP cc_start: 0.8619 (p0) cc_final: 0.8408 (p0) REVERT: h 105 GLU cc_start: 0.8526 (tp30) cc_final: 0.8152 (tp30) REVERT: h 108 LYS cc_start: 0.9413 (ptpt) cc_final: 0.9175 (ptpp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1281 time to fit residues: 27.7699 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS ** e 113 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 = 0.3457 r_free = 0.3457 target = 0.042371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034597 restraints weight = 125668.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.035502 restraints weight = 69747.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.036125 restraints weight = 47937.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.036472 restraints weight = 37388.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.036758 restraints weight = 32291.947| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14386 Z= 0.165 Angle : 0.732 10.282 20853 Z= 0.417 Chirality : 0.047 0.306 2376 Planarity : 0.005 0.061 1478 Dihedral : 32.278 175.798 4581 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.87 % Allowed : 9.96 % Favored : 89.18 % 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: 0.25 (0.27), residues: 825 helix: 0.61 (0.20), residues: 580 sheet: -0.65 (1.79), residues: 10 loop : -0.70 (0.35), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 42 TYR 0.040 0.003 TYR h 83 PHE 0.008 0.001 PHE e 104 HIS 0.003 0.001 HIS h 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.17 (14386) covalent geometry : angle 0.73233 / 0.42 (20853) hydrogen bonds : bond 0.04827 / 3.29 ( 856) hydrogen bonds : angle 3.75680 / 2.76 ( 2133) *********************** 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 134 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.8803 (m-80) cc_final: 0.8458 (m-80) REVERT: a 79 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8156 (tmtt) REVERT: a 80 THR cc_start: 0.7953 (p) cc_final: 0.7573 (p) REVERT: a 81 ASP cc_start: 0.8499 (p0) cc_final: 0.8279 (p0) REVERT: a 97 GLU cc_start: 0.7673 (tt0) cc_final: 0.7467 (tt0) REVERT: b 85 ASP cc_start: 0.7830 (m-30) cc_final: 0.7583 (m-30) REVERT: b 97 LEU cc_start: 0.8453 (tp) cc_final: 0.8123 (tp) REVERT: c 36 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8618 (mmmt) REVERT: d 102 LEU cc_start: 0.9482 (mm) cc_final: 0.9082 (mp) REVERT: g 61 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8412 (tm-30) REVERT: g 62 ILE cc_start: 0.9496 (pt) cc_final: 0.9028 (pt) REVERT: g 95 LYS cc_start: 0.8829 (tptt) cc_final: 0.8184 (mmmm) REVERT: h 33 ARG cc_start: 0.6407 (mtp-110) cc_final: 0.5574 (mtt180) REVERT: h 51 ASP cc_start: 0.8556 (p0) cc_final: 0.8224 (p0) REVERT: h 105 GLU cc_start: 0.8555 (tp30) cc_final: 0.8259 (tp30) REVERT: h 108 LYS cc_start: 0.9308 (ptpt) cc_final: 0.9063 (ptpp) outliers start: 6 outliers final: 5 residues processed: 132 average time/residue: 0.1320 time to fit residues: 24.9905 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 68 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 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 = 0.3443 r_free = 0.3443 target = 0.041930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.034086 restraints weight = 125247.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.035008 restraints weight = 68724.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.035632 restraints weight = 47040.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.036045 restraints weight = 36521.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036319 restraints weight = 30805.407| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14386 Z= 0.164 Angle : 0.688 9.805 20853 Z= 0.395 Chirality : 0.045 0.309 2376 Planarity : 0.005 0.074 1478 Dihedral : 32.140 177.682 4581 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.44 % Allowed : 12.41 % Favored : 86.15 % 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: 0.63 (0.27), residues: 825 helix: 0.93 (0.20), residues: 584 sheet: -0.78 (1.75), residues: 10 loop : -0.68 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 131 TYR 0.041 0.002 TYR h 83 PHE 0.012 0.001 PHE e 78 HIS 0.003 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (14386) covalent geometry : angle 0.68763 / 0.40 (20853) hydrogen bonds : bond 0.04867 / 3.29 ( 856) hydrogen bonds : angle 3.56265 / 2.62 ( 2133) *********************** 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 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.8844 (m-80) cc_final: 0.8451 (m-80) REVERT: a 97 GLU cc_start: 0.7779 (tt0) cc_final: 0.7525 (tt0) REVERT: c 36 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8599 (mmmt) REVERT: d 102 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9047 (mp) REVERT: e 97 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8088 (mt-10) REVERT: e 120 MET cc_start: 0.7203 (mtt) cc_final: 0.6915 (mtt) REVERT: f 63 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8695 (mm-30) REVERT: f 90 LEU cc_start: 0.8805 (mm) cc_final: 0.8584 (mm) REVERT: g 61 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8470 (tm-30) REVERT: g 62 ILE cc_start: 0.9518 (pt) cc_final: 0.9123 (pt) REVERT: g 95 LYS cc_start: 0.8821 (tptt) cc_final: 0.8198 (mmmm) REVERT: h 33 ARG cc_start: 0.6400 (mtp-110) cc_final: 0.5705 (mtt-85) REVERT: h 51 ASP cc_start: 0.8579 (p0) cc_final: 0.8274 (p0) REVERT: h 105 GLU cc_start: 0.8623 (tp30) cc_final: 0.8272 (tp30) REVERT: h 108 LYS cc_start: 0.9319 (ptpt) cc_final: 0.8905 (ptpp) outliers start: 10 outliers final: 7 residues processed: 125 average time/residue: 0.1217 time to fit residues: 21.9948 Evaluate side-chains 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 49 optimal weight: 0.4980 chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 76 GLN a 108 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** 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 = 0.3431 r_free = 0.3431 target = 0.041290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.033304 restraints weight = 126576.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.034193 restraints weight = 69852.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.034791 restraints weight = 48128.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.035196 restraints weight = 37811.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.035477 restraints weight = 32167.459| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14386 Z= 0.174 Angle : 0.681 9.454 20853 Z= 0.388 Chirality : 0.044 0.305 2376 Planarity : 0.005 0.061 1478 Dihedral : 32.059 176.942 4581 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.02 % Allowed : 11.40 % Favored : 86.58 % 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: 0.92 (0.28), residues: 825 helix: 1.18 (0.21), residues: 580 sheet: -1.02 (1.75), residues: 10 loop : -0.60 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 29 TYR 0.040 0.002 TYR h 83 PHE 0.008 0.001 PHE g 25 HIS 0.005 0.001 HIS e 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (14386) covalent geometry : angle 0.68142 / 0.39 (20853) hydrogen bonds : bond 0.05081 / 3.46 ( 856) hydrogen bonds : angle 3.46037 / 2.55 ( 2133) *********************** 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 128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.8826 (m-80) cc_final: 0.8472 (m-80) REVERT: a 97 GLU cc_start: 0.7766 (tt0) cc_final: 0.7529 (tt0) REVERT: b 97 LEU cc_start: 0.8885 (tp) cc_final: 0.8659 (tp) REVERT: c 36 LYS cc_start: 0.9054 (mmpt) cc_final: 0.8624 (mmmt) REVERT: d 59 MET cc_start: 0.8546 (tpt) cc_final: 0.7851 (tpt) REVERT: e 97 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7542 (mp0) REVERT: f 63 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8698 (mm-30) REVERT: f 90 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8549 (mm) REVERT: g 61 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8497 (tm-30) REVERT: g 62 ILE cc_start: 0.9535 (pt) cc_final: 0.9166 (pt) REVERT: g 95 LYS cc_start: 0.8895 (tptt) cc_final: 0.8240 (mmmm) REVERT: h 33 ARG cc_start: 0.6522 (mtp-110) cc_final: 0.5693 (mtt-85) REVERT: h 51 ASP cc_start: 0.8590 (p0) cc_final: 0.8320 (p0) REVERT: h 105 GLU cc_start: 0.8606 (tp30) cc_final: 0.8293 (tp30) REVERT: h 108 LYS cc_start: 0.9282 (ptpt) cc_final: 0.8884 (ptpp) outliers start: 14 outliers final: 8 residues processed: 121 average time/residue: 0.1197 time to fit residues: 21.1578 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 68 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.041668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.033682 restraints weight = 126974.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.034599 restraints weight = 69925.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.035197 restraints weight = 47930.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.035613 restraints weight = 37608.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.035907 restraints weight = 31919.376| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14386 Z= 0.147 Angle : 0.659 10.503 20853 Z= 0.376 Chirality : 0.043 0.303 2376 Planarity : 0.004 0.059 1478 Dihedral : 31.974 176.659 4581 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.87 % Allowed : 14.29 % Favored : 84.85 % 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: 1.10 (0.28), residues: 825 helix: 1.29 (0.21), residues: 588 sheet: -1.05 (1.73), residues: 10 loop : -0.53 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 99 TYR 0.039 0.002 TYR h 83 PHE 0.006 0.001 PHE a 104 HIS 0.003 0.001 HIS e 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (14386) covalent geometry : angle 0.65937 / 0.38 (20853) hydrogen bonds : bond 0.04191 / 2.86 ( 856) hydrogen bonds : angle 3.35797 / 2.47 ( 2133) *********************** 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 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.8795 (m-80) cc_final: 0.8488 (m-80) REVERT: b 74 GLU cc_start: 0.8906 (pt0) cc_final: 0.8684 (pm20) REVERT: c 36 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8603 (mmmt) REVERT: d 102 LEU cc_start: 0.9439 (mm) cc_final: 0.9108 (mp) REVERT: e 97 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7872 (mt-10) REVERT: f 63 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8565 (mm-30) REVERT: f 90 LEU cc_start: 0.8708 (mm) cc_final: 0.8490 (mm) REVERT: g 61 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8473 (tm-30) REVERT: g 62 ILE cc_start: 0.9539 (pt) cc_final: 0.9164 (pt) REVERT: g 95 LYS cc_start: 0.8824 (tptt) cc_final: 0.8182 (mmmm) REVERT: h 33 ARG cc_start: 0.6696 (mtp-110) cc_final: 0.5503 (mtt-85) REVERT: h 51 ASP cc_start: 0.8577 (p0) cc_final: 0.8284 (p0) REVERT: h 105 GLU cc_start: 0.8603 (tp30) cc_final: 0.8300 (tp30) REVERT: h 108 LYS cc_start: 0.9261 (ptpt) cc_final: 0.8850 (ptpp) outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 0.1189 time to fit residues: 21.5567 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain f residue 74 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 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 = 0.3451 r_free = 0.3451 target = 0.041998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.034031 restraints weight = 125493.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.034938 restraints weight = 69380.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.035557 restraints weight = 47697.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.035940 restraints weight = 37260.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.036220 restraints weight = 31909.535| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14386 Z= 0.140 Angle : 0.659 10.544 20853 Z= 0.375 Chirality : 0.043 0.296 2376 Planarity : 0.004 0.059 1478 Dihedral : 31.889 176.984 4581 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.15 % Allowed : 15.87 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.28), residues: 825 helix: 1.30 (0.21), residues: 586 sheet: -1.01 (1.73), residues: 10 loop : -0.47 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 42 TYR 0.038 0.002 TYR h 83 PHE 0.014 0.001 PHE d 65 HIS 0.002 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (14386) covalent geometry : angle 0.65895 / 0.37 (20853) hydrogen bonds : bond 0.04079 / 2.77 ( 856) hydrogen bonds : angle 3.35439 / 2.48 ( 2133) *********************** 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 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 74 GLU cc_start: 0.8941 (pt0) cc_final: 0.8679 (pm20) REVERT: b 97 LEU cc_start: 0.8528 (tp) cc_final: 0.8323 (tp) REVERT: c 36 LYS cc_start: 0.9015 (mmpt) cc_final: 0.8602 (mmmt) REVERT: c 61 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7923 (tm-30) REVERT: e 97 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7737 (mt-10) REVERT: f 63 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8529 (mm-30) REVERT: f 90 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (mm) REVERT: g 61 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8502 (tm-30) REVERT: g 62 ILE cc_start: 0.9537 (pt) cc_final: 0.9164 (pt) REVERT: g 95 LYS cc_start: 0.8806 (tptt) cc_final: 0.8181 (mmmm) REVERT: h 33 ARG cc_start: 0.6599 (mtp-110) cc_final: 0.5376 (mtt-85) REVERT: h 51 ASP cc_start: 0.8602 (p0) cc_final: 0.8302 (p0) REVERT: h 105 GLU cc_start: 0.8609 (tp30) cc_final: 0.8310 (tp30) REVERT: h 108 LYS cc_start: 0.9260 (ptpt) cc_final: 0.8924 (ptpp) outliers start: 8 outliers final: 4 residues processed: 122 average time/residue: 0.1137 time to fit residues: 20.7046 Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain f residue 90 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.039632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.031805 restraints weight = 131394.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.032661 restraints weight = 72699.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.033237 restraints weight = 50230.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.033616 restraints weight = 39448.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.033888 restraints weight = 33741.341| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 14386 Z= 0.263 Angle : 0.747 10.846 20853 Z= 0.415 Chirality : 0.045 0.254 2376 Planarity : 0.005 0.063 1478 Dihedral : 32.075 177.485 4581 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.02 % Allowed : 17.17 % Favored : 80.81 % 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: 0.98 (0.28), residues: 825 helix: 1.18 (0.20), residues: 584 sheet: -0.84 (1.86), residues: 10 loop : -0.47 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 131 TYR 0.041 0.003 TYR h 83 PHE 0.016 0.002 PHE g 25 HIS 0.004 0.001 HIS c 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.26 (14386) covalent geometry : angle 0.74695 / 0.42 (20853) hydrogen bonds : bond 0.08322 / 5.59 ( 856) hydrogen bonds : angle 3.62547 / 2.66 ( 2133) *********************** 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 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 122 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8082 (ptmm) REVERT: c 36 LYS cc_start: 0.9129 (mmpt) cc_final: 0.8705 (mmmt) REVERT: e 97 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7896 (mt-10) REVERT: f 63 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8590 (mm-30) REVERT: f 90 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8639 (mm) REVERT: g 61 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8524 (tm-30) REVERT: g 62 ILE cc_start: 0.9542 (pt) cc_final: 0.9197 (pt) REVERT: g 95 LYS cc_start: 0.8929 (tptt) cc_final: 0.8318 (mmmm) REVERT: h 51 ASP cc_start: 0.8556 (p0) cc_final: 0.8338 (p0) REVERT: h 105 GLU cc_start: 0.8684 (tp30) cc_final: 0.8423 (tp30) REVERT: h 108 LYS cc_start: 0.9267 (ptpt) cc_final: 0.9015 (ptpp) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.1298 time to fit residues: 19.9621 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain b residue 68 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** 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 = 0.3406 r_free = 0.3406 target = 0.040475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.032550 restraints weight = 127002.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.033421 restraints weight = 70230.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.034007 restraints weight = 48487.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034408 restraints weight = 38090.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.034694 restraints weight = 32529.551| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14386 Z= 0.166 Angle : 0.685 11.452 20853 Z= 0.385 Chirality : 0.043 0.268 2376 Planarity : 0.004 0.056 1478 Dihedral : 32.076 176.970 4581 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.87 % Allowed : 18.33 % Favored : 80.81 % 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: 1.06 (0.28), residues: 825 helix: 1.25 (0.21), residues: 586 sheet: -0.66 (1.93), residues: 10 loop : -0.52 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 79 TYR 0.043 0.002 TYR h 83 PHE 0.006 0.001 PHE c 25 HIS 0.003 0.001 HIS e 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (14386) covalent geometry : angle 0.68475 / 0.38 (20853) hydrogen bonds : bond 0.04722 / 3.22 ( 856) hydrogen bonds : angle 3.45977 / 2.54 ( 2133) *********************** 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 LYS cc_start: 0.9101 (mmpt) cc_final: 0.8673 (mmmt) REVERT: c 61 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7914 (tm-30) REVERT: e 97 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7837 (mt-10) REVERT: f 90 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8639 (mm) REVERT: g 61 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8506 (tm-30) REVERT: g 62 ILE cc_start: 0.9542 (pt) cc_final: 0.9201 (pt) REVERT: g 95 LYS cc_start: 0.8858 (tptt) cc_final: 0.8227 (mmmm) REVERT: h 51 ASP cc_start: 0.8548 (p0) cc_final: 0.8299 (p0) REVERT: h 105 GLU cc_start: 0.8649 (tp30) cc_final: 0.8362 (tp30) REVERT: h 108 LYS cc_start: 0.9237 (ptpt) cc_final: 0.8899 (ptpp) outliers start: 6 outliers final: 5 residues processed: 111 average time/residue: 0.1134 time to fit residues: 18.6843 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 105 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 84 optimal weight: 30.0000 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 108 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 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 = 0.3434 r_free = 0.3434 target = 0.041404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.033508 restraints weight = 126924.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.034408 restraints weight = 70042.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.035014 restraints weight = 48080.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.035434 restraints weight = 37682.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.035717 restraints weight = 31937.928| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14386 Z= 0.142 Angle : 0.678 11.635 20853 Z= 0.380 Chirality : 0.043 0.264 2376 Planarity : 0.004 0.055 1478 Dihedral : 31.886 177.631 4581 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.01 % Allowed : 18.33 % Favored : 80.66 % 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: 1.11 (0.28), residues: 825 helix: 1.26 (0.21), residues: 584 sheet: -0.87 (1.84), residues: 10 loop : -0.38 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 79 TYR 0.039 0.002 TYR h 83 PHE 0.017 0.001 PHE d 65 HIS 0.003 0.001 HIS e 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (14386) covalent geometry : angle 0.67842 / 0.38 (20853) hydrogen bonds : bond 0.04039 / 2.75 ( 856) hydrogen bonds : angle 3.41285 / 2.51 ( 2133) *********************** 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 121 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 97 LEU cc_start: 0.8723 (tp) cc_final: 0.8472 (tp) REVERT: c 36 LYS cc_start: 0.9046 (mmpt) cc_final: 0.8627 (mmmt) REVERT: d 35 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6298 (tt0) REVERT: d 108 LYS cc_start: 0.9279 (pttm) cc_final: 0.9064 (pttm) REVERT: e 97 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7865 (mt-10) REVERT: f 90 LEU cc_start: 0.8772 (mm) cc_final: 0.8538 (mm) REVERT: g 61 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8483 (tm-30) REVERT: g 62 ILE cc_start: 0.9534 (pt) cc_final: 0.9170 (pt) REVERT: g 95 LYS cc_start: 0.8824 (tptt) cc_final: 0.8189 (mmmm) REVERT: h 51 ASP cc_start: 0.8568 (p0) cc_final: 0.8257 (p0) REVERT: h 105 GLU cc_start: 0.8577 (tp30) cc_final: 0.8256 (tp30) REVERT: h 108 LYS cc_start: 0.9237 (ptpt) cc_final: 0.8803 (ptpp) outliers start: 7 outliers final: 5 residues processed: 119 average time/residue: 0.1133 time to fit residues: 19.9242 Evaluate side-chains 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.0470 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 29 optimal weight: 0.0670 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 108 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 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 = 0.3414 r_free = 0.3414 target = 0.040759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032901 restraints weight = 127565.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.033776 restraints weight = 70790.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034376 restraints weight = 48916.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.034789 restraints weight = 38245.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.035070 restraints weight = 32515.711| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14386 Z= 0.165 Angle : 0.693 13.373 20853 Z= 0.386 Chirality : 0.042 0.260 2376 Planarity : 0.004 0.059 1478 Dihedral : 31.875 177.733 4581 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.87 % Allowed : 18.61 % Favored : 80.52 % 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: 1.12 (0.28), residues: 825 helix: 1.26 (0.21), residues: 584 sheet: -0.95 (1.80), residues: 10 loop : -0.35 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 131 TYR 0.047 0.002 TYR h 83 PHE 0.008 0.001 PHE g 25 HIS 0.003 0.001 HIS e 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (14386) covalent geometry : angle 0.69285 / 0.39 (20853) hydrogen bonds : bond 0.04935 / 3.33 ( 856) hydrogen bonds : angle 3.45540 / 2.52 ( 2133) ********************** 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 LYS cc_start: 0.9089 (mmpt) cc_final: 0.8681 (mmmt) REVERT: c 61 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7939 (tm-30) REVERT: d 35 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6395 (tt0) REVERT: d 108 LYS cc_start: 0.9292 (pttm) cc_final: 0.9091 (pttm) REVERT: e 97 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7847 (mt-10) REVERT: f 90 LEU cc_start: 0.8801 (mm) cc_final: 0.8570 (mm) REVERT: g 61 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8505 (tm-30) REVERT: g 62 ILE cc_start: 0.9543 (pt) cc_final: 0.9190 (pt) REVERT: g 95 LYS cc_start: 0.8858 (tptt) cc_final: 0.8218 (mmmm) REVERT: h 51 ASP cc_start: 0.8543 (p0) cc_final: 0.8267 (p0) REVERT: h 105 GLU cc_start: 0.8600 (tp30) cc_final: 0.8330 (tp30) REVERT: h 108 LYS cc_start: 0.9240 (ptpt) cc_final: 0.8900 (ptpp) outliers start: 6 outliers final: 5 residues processed: 112 average time/residue: 0.1183 time to fit residues: 19.4814 Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** 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 = 0.3442 r_free = 0.3442 target = 0.044133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.036779 restraints weight = 136789.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.037650 restraints weight = 73712.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.038171 restraints weight = 50232.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.038565 restraints weight = 40205.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.038870 restraints weight = 33498.439| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14386 Z= 0.176 Angle : 0.692 11.714 20853 Z= 0.389 Chirality : 0.043 0.264 2376 Planarity : 0.004 0.058 1478 Dihedral : 31.932 177.954 4581 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.01 % Allowed : 18.04 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.28), residues: 825 helix: 1.20 (0.21), residues: 584 sheet: -0.96 (1.79), residues: 10 loop : -0.36 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 79 TYR 0.040 0.002 TYR h 83 PHE 0.020 0.001 PHE d 65 HIS 0.003 0.001 HIS e 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (14386) covalent geometry : angle 0.69154 / 0.39 (20853) hydrogen bonds : bond 0.05034 / 3.40 ( 856) hydrogen bonds : angle 3.55365 / 2.60 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.34 seconds wall clock time: 34 minutes 1.06 seconds (2041.06 seconds total)