Starting phenix.real_space_refine on Wed Mar 4 17:09:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf5_13368/03_2026/7pf5_13368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf5_13368/03_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_13368/03_2026/7pf5_13368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf5_13368/03_2026/7pf5_13368.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf5_13368/03_2026/7pf5_13368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf5_13368/03_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-dev-5986/lib/python3.9/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: 2.82, 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: 1.18 Conformation dependent library (CDL) restraints added in 525.5 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: 2.35 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: 3.52 Time building geometry restraints manager: 1.60 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' DG J 541 " pdb=" O3' DG J 541 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.31e+00 bond pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CG GLU b 53 " pdb=" CD GLU b 53 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.10e+00 bond pdb=" CB GLU b 53 " pdb=" CG GLU b 53 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.06e+00 bond pdb=" C3' DG I 223 " pdb=" O3' DG I 223 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.50e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 20149 2.17 - 4.33: 616 4.33 - 6.50: 64 6.50 - 8.67: 18 8.67 - 10.84: 6 Bond angle restraints: 20853 Sorted by residual: angle pdb=" CB ARG c 42 " pdb=" CG ARG c 42 " pdb=" CD ARG c 42 " ideal model delta sigma weight residual 111.30 121.64 -10.34 2.30e+00 1.89e-01 2.02e+01 angle pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta sigma weight residual 120.31 114.28 6.03 1.52e+00 4.33e-01 1.57e+01 angle pdb=" N GLN e 55 " pdb=" CA GLN e 55 " pdb=" CB GLN e 55 " ideal model delta sigma weight residual 110.28 116.01 -5.73 1.55e+00 4.16e-01 1.37e+01 angle pdb=" CB MET b 84 " pdb=" CG MET b 84 " pdb=" SD MET b 84 " ideal model delta sigma weight residual 112.70 123.54 -10.84 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET h 62 " pdb=" CG MET h 62 " pdb=" SD MET h 62 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+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: 1769 0.048 - 0.096: 476 0.096 - 0.144: 103 0.144 - 0.192: 20 0.192 - 0.239: 8 Chirality restraints: 2376 Sorted by residual: 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 chirality pdb=" CG LEU a 92 " pdb=" CB LEU a 92 " pdb=" CD1 LEU a 92 " pdb=" CD2 LEU a 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+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: 2.820 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14386 Z= 0.267 Angle : 0.889 10.836 20853 Z= 0.497 Chirality : 0.048 0.239 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 covalent geometry : bond 0.00604 (14386) covalent geometry : angle 0.88856 (20853) hydrogen bonds : bond 0.09845 ( 856) hydrogen bonds : angle 4.76893 ( 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 : 0.373 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: 0.8021 (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: 0.9197 (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: 0.6114 (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: 0.1191 time to fit residues: 25.7424 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 : 0.285 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 20.0000 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: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 76 GLN a 108 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 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 = 0.3465 r_free = 0.3465 target = 0.042417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.034585 restraints weight = 126456.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.035463 restraints weight = 71208.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.036039 restraints weight = 49438.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.036430 restraints weight = 39087.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.036704 restraints weight = 33346.443| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14386 Z= 0.167 Angle : 0.622 9.174 20853 Z= 0.365 Chirality : 0.035 0.156 2376 Planarity : 0.005 0.057 1478 Dihedral : 31.588 179.705 4581 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 0.69 (0.27), residues: 825 helix: 0.92 (0.20), residues: 586 sheet: -0.10 (1.97), residues: 10 loop : -0.55 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 99 TYR 0.023 0.002 TYR c 57 PHE 0.007 0.001 PHE e 104 HIS 0.003 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00361 (14386) covalent geometry : angle 0.62151 (20853) hydrogen bonds : bond 0.03856 ( 856) hydrogen bonds : angle 3.41362 ( 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 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 81 ASP cc_start: 0.8514 (p0) cc_final: 0.8308 (p0) REVERT: c 36 LYS cc_start: 0.9015 (mmpt) cc_final: 0.8602 (mmmt) REVERT: d 65 PHE cc_start: 0.8799 (t80) cc_final: 0.8572 (t80) REVERT: d 105 GLU cc_start: 0.8367 (pm20) cc_final: 0.8087 (pm20) REVERT: f 90 LEU cc_start: 0.8789 (mm) cc_final: 0.8578 (mm) REVERT: g 61 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8244 (tm-30) REVERT: g 62 ILE cc_start: 0.9497 (pt) cc_final: 0.9081 (pt) REVERT: g 95 LYS cc_start: 0.8812 (tptt) cc_final: 0.8148 (mmmm) REVERT: h 33 ARG cc_start: 0.6311 (mtp-110) cc_final: 0.5589 (mtt-85) REVERT: h 51 ASP cc_start: 0.8520 (p0) cc_final: 0.8169 (p0) REVERT: h 108 LYS cc_start: 0.9173 (ptpt) cc_final: 0.8949 (pttm) outliers start: 6 outliers final: 4 residues processed: 137 average time/residue: 0.1183 time to fit residues: 23.2745 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain f residue 22 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 0.0970 chunk 98 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.042685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.034836 restraints weight = 129348.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.035741 restraints weight = 72668.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.036334 restraints weight = 50122.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.036741 restraints weight = 39547.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.037032 restraints weight = 33653.064| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14386 Z= 0.157 Angle : 0.597 9.937 20853 Z= 0.350 Chirality : 0.034 0.149 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.349 175.657 4581 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 1.09 (0.28), residues: 825 helix: 1.25 (0.21), residues: 584 sheet: -0.37 (1.89), residues: 10 loop : -0.44 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 131 TYR 0.026 0.002 TYR h 83 PHE 0.009 0.001 PHE e 104 HIS 0.004 0.001 HIS e 113 Details of bonding type rmsd covalent geometry : bond 0.00342 (14386) covalent geometry : angle 0.59658 (20853) hydrogen bonds : bond 0.03548 ( 856) hydrogen bonds : angle 3.23215 ( 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 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8360 (tmtt) REVERT: c 30 VAL cc_start: 0.8777 (t) cc_final: 0.8555 (t) REVERT: c 36 LYS cc_start: 0.9005 (mmpt) cc_final: 0.8595 (mmmt) REVERT: c 61 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7835 (tm-30) REVERT: e 97 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7808 (mt-10) REVERT: f 90 LEU cc_start: 0.8755 (mm) cc_final: 0.8517 (mm) REVERT: g 61 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8490 (tm-30) REVERT: g 62 ILE cc_start: 0.9493 (pt) cc_final: 0.9103 (pt) REVERT: g 65 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8935 (mm) REVERT: h 33 ARG cc_start: 0.6186 (mtp-110) cc_final: 0.5451 (mtt-85) REVERT: h 51 ASP cc_start: 0.8450 (p0) cc_final: 0.8114 (p0) outliers start: 10 outliers final: 7 residues processed: 136 average time/residue: 0.1188 time to fit residues: 23.6911 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 65 LEU 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: 7.9990 chunk 43 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS u 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.040325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.032469 restraints weight = 129463.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.033355 restraints weight = 71538.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.033953 restraints weight = 49089.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.034353 restraints weight = 38372.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.034559 restraints weight = 32741.134| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14386 Z= 0.237 Angle : 0.631 10.625 20853 Z= 0.369 Chirality : 0.036 0.204 2376 Planarity : 0.005 0.058 1478 Dihedral : 31.521 175.164 4581 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.28), residues: 825 helix: 1.31 (0.21), residues: 588 sheet: -0.83 (1.83), residues: 10 loop : -0.42 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 131 TYR 0.016 0.002 TYR c 39 PHE 0.021 0.002 PHE d 65 HIS 0.005 0.001 HIS h 109 Details of bonding type rmsd covalent geometry : bond 0.00522 (14386) covalent geometry : angle 0.63096 (20853) hydrogen bonds : bond 0.05467 ( 856) hydrogen bonds : angle 3.39882 ( 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 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8153 (tmtt) REVERT: a 81 ASP cc_start: 0.8423 (p0) cc_final: 0.8203 (p0) REVERT: c 36 LYS cc_start: 0.9107 (mmpt) cc_final: 0.8678 (mmmt) REVERT: e 97 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7399 (mp0) REVERT: g 61 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8651 (tm-30) REVERT: g 62 ILE cc_start: 0.9552 (pt) cc_final: 0.9258 (pt) REVERT: h 51 ASP cc_start: 0.8478 (p0) cc_final: 0.8218 (p0) REVERT: h 109 HIS cc_start: 0.8435 (m170) cc_final: 0.7880 (m90) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.1201 time to fit residues: 21.0759 Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 54 VAL 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: 3.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN b 25 ASN ** 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 = 0.3411 r_free = 0.3411 target = 0.040699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.033096 restraints weight = 128955.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.034007 restraints weight = 70728.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.034614 restraints weight = 47923.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.035011 restraints weight = 36995.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.035290 restraints weight = 31323.382| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14386 Z= 0.188 Angle : 0.609 11.070 20853 Z= 0.356 Chirality : 0.034 0.189 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.407 176.519 4581 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.16 % Allowed : 16.16 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.28), residues: 825 helix: 1.37 (0.21), residues: 588 sheet: -1.08 (1.75), residues: 10 loop : -0.39 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 95 TYR 0.012 0.002 TYR a 54 PHE 0.006 0.001 PHE g 25 HIS 0.002 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (14386) covalent geometry : angle 0.60910 (20853) hydrogen bonds : bond 0.04166 ( 856) hydrogen bonds : angle 3.30544 ( 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 132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.8901 (tmtt) cc_final: 0.8189 (tmtt) REVERT: a 81 ASP cc_start: 0.8405 (p0) cc_final: 0.8196 (p0) REVERT: c 36 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8685 (mmmt) REVERT: c 61 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7891 (tm-30) REVERT: e 97 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7711 (mt-10) REVERT: f 63 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8656 (mm-30) REVERT: g 61 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8228 (tm-30) REVERT: g 62 ILE cc_start: 0.9556 (pt) cc_final: 0.9120 (pt) REVERT: g 65 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8919 (mm) REVERT: h 51 ASP cc_start: 0.8481 (p0) cc_final: 0.8178 (p0) REVERT: h 109 HIS cc_start: 0.8460 (m170) cc_final: 0.7922 (m90) outliers start: 15 outliers final: 9 residues processed: 125 average time/residue: 0.1209 time to fit residues: 22.0641 Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 76 THR 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: 1.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3423 r_free = 0.3423 target = 0.041092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.033531 restraints weight = 127780.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034442 restraints weight = 70462.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.035053 restraints weight = 47927.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.035463 restraints weight = 36977.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.035760 restraints weight = 31228.219| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14386 Z= 0.167 Angle : 0.607 11.408 20853 Z= 0.352 Chirality : 0.034 0.194 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.270 176.488 4581 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 17.32 % Favored : 81.24 % 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: 1.21 (0.28), residues: 825 helix: 1.34 (0.21), residues: 588 sheet: -1.07 (1.78), residues: 10 loop : -0.38 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 131 TYR 0.017 0.002 TYR b 88 PHE 0.010 0.001 PHE a 84 HIS 0.002 0.001 HIS e 113 Details of bonding type rmsd covalent geometry : bond 0.00367 (14386) covalent geometry : angle 0.60661 (20853) hydrogen bonds : bond 0.03793 ( 856) hydrogen bonds : angle 3.30530 ( 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 131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.8936 (tmtt) cc_final: 0.8262 (tmtt) REVERT: c 36 LYS cc_start: 0.9029 (mmpt) cc_final: 0.8627 (mmmt) REVERT: e 97 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7568 (mt-10) REVERT: f 63 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8632 (mm-30) REVERT: g 61 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8270 (tm-30) REVERT: g 62 ILE cc_start: 0.9545 (pt) cc_final: 0.9090 (pt) REVERT: g 65 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8930 (mm) REVERT: h 51 ASP cc_start: 0.8488 (p0) cc_final: 0.8224 (p0) REVERT: h 109 HIS cc_start: 0.8434 (m170) cc_final: 0.7918 (m90) outliers start: 10 outliers final: 8 residues processed: 127 average time/residue: 0.1170 time to fit residues: 21.8210 Evaluate side-chains 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 65 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3354 r_free = 0.3354 target = 0.038675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.031200 restraints weight = 132274.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.032033 restraints weight = 73347.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.032618 restraints weight = 50149.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.032938 restraints weight = 38868.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.033223 restraints weight = 33664.030| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14386 Z= 0.254 Angle : 0.664 11.807 20853 Z= 0.383 Chirality : 0.036 0.197 2376 Planarity : 0.005 0.056 1478 Dihedral : 31.695 176.735 4581 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.88 % Allowed : 18.18 % Favored : 79.94 % 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 (0.28), residues: 825 helix: 1.10 (0.21), residues: 586 sheet: -0.98 (1.82), residues: 10 loop : -0.47 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 52 TYR 0.017 0.002 TYR a 54 PHE 0.010 0.002 PHE a 67 HIS 0.003 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00560 (14386) covalent geometry : angle 0.66438 (20853) hydrogen bonds : bond 0.05702 ( 856) hydrogen bonds : angle 3.57743 ( 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 122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.9091 (tmtt) cc_final: 0.8440 (tmtt) REVERT: a 81 ASP cc_start: 0.8634 (p0) cc_final: 0.8388 (p0) REVERT: b 91 LYS cc_start: 0.9425 (ttpp) cc_final: 0.9212 (tttm) REVERT: c 36 LYS cc_start: 0.9094 (mmpt) cc_final: 0.8689 (mmmt) REVERT: c 41 GLU cc_start: 0.8350 (mp0) cc_final: 0.7990 (pm20) REVERT: c 61 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7890 (tm-30) REVERT: c 91 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8526 (tm-30) REVERT: d 76 GLU cc_start: 0.8191 (tp30) cc_final: 0.7839 (tp30) REVERT: d 102 LEU cc_start: 0.9473 (mm) cc_final: 0.9209 (mp) REVERT: e 97 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7737 (mt-10) REVERT: g 61 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8222 (tm-30) REVERT: g 62 ILE cc_start: 0.9571 (pt) cc_final: 0.9131 (pt) REVERT: g 65 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8938 (mm) REVERT: h 51 ASP cc_start: 0.8516 (p0) cc_final: 0.8287 (p0) REVERT: h 109 HIS cc_start: 0.8469 (m170) cc_final: 0.7937 (m90) outliers start: 13 outliers final: 12 residues processed: 117 average time/residue: 0.1289 time to fit residues: 21.6500 Evaluate side-chains 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3409 r_free = 0.3409 target = 0.040531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.032934 restraints weight = 125628.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033833 restraints weight = 69179.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.034429 restraints weight = 47028.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.034845 restraints weight = 36555.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.035146 restraints weight = 30755.970| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14386 Z= 0.166 Angle : 0.627 11.730 20853 Z= 0.362 Chirality : 0.034 0.179 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.385 177.049 4581 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.44 % Allowed : 19.34 % Favored : 79.22 % 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: 1.08 (0.28), residues: 825 helix: 1.25 (0.21), residues: 588 sheet: -1.23 (1.72), residues: 10 loop : -0.45 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 42 TYR 0.030 0.002 TYR b 88 PHE 0.040 0.002 PHE e 104 HIS 0.002 0.001 HIS d 109 Details of bonding type rmsd covalent geometry : bond 0.00367 (14386) covalent geometry : angle 0.62697 (20853) hydrogen bonds : bond 0.03649 ( 856) hydrogen bonds : angle 3.38699 ( 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 130 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.9025 (tmtt) cc_final: 0.8461 (tmtt) REVERT: c 36 LYS cc_start: 0.9024 (mmpt) cc_final: 0.8620 (mmmt) REVERT: c 91 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8476 (tm-30) REVERT: e 97 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7762 (mt-10) REVERT: e 123 ASP cc_start: 0.8027 (m-30) cc_final: 0.7821 (m-30) REVERT: g 61 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8213 (tm-30) REVERT: g 62 ILE cc_start: 0.9551 (pt) cc_final: 0.9120 (pt) REVERT: g 65 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8944 (mm) REVERT: h 51 ASP cc_start: 0.8420 (p0) cc_final: 0.8111 (p0) REVERT: h 105 GLU cc_start: 0.8545 (tp30) cc_final: 0.8327 (tp30) REVERT: u 53 ARG cc_start: 0.3872 (tpt170) cc_final: 0.3636 (tpt170) outliers start: 10 outliers final: 9 residues processed: 124 average time/residue: 0.1308 time to fit residues: 23.2506 Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3368 r_free = 0.3368 target = 0.039151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.031637 restraints weight = 131658.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032493 restraints weight = 72667.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.033082 restraints weight = 49692.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.033473 restraints weight = 38572.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.033761 restraints weight = 32764.939| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14386 Z= 0.225 Angle : 0.656 12.063 20853 Z= 0.377 Chirality : 0.036 0.202 2376 Planarity : 0.004 0.055 1478 Dihedral : 31.615 177.002 4581 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 19.91 % Favored : 78.64 % 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: 1.00 (0.28), residues: 825 helix: 1.18 (0.21), residues: 586 sheet: -0.95 (1.82), residues: 10 loop : -0.46 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 79 TYR 0.021 0.002 TYR a 54 PHE 0.007 0.001 PHE a 104 HIS 0.003 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00496 (14386) covalent geometry : angle 0.65626 (20853) hydrogen bonds : bond 0.05106 ( 856) hydrogen bonds : angle 3.53679 ( 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 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.8959 (tmtt) cc_final: 0.8366 (tmtt) REVERT: a 81 ASP cc_start: 0.8713 (p0) cc_final: 0.8468 (p0) REVERT: b 91 LYS cc_start: 0.9400 (ttpp) cc_final: 0.9110 (tttm) REVERT: c 36 LYS cc_start: 0.9073 (mmpt) cc_final: 0.8672 (mmmt) REVERT: c 61 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7889 (tm-30) REVERT: c 91 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8517 (tm-30) REVERT: d 102 LEU cc_start: 0.9415 (mm) cc_final: 0.9174 (mp) REVERT: e 97 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7731 (mt-10) REVERT: g 61 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8235 (tm-30) REVERT: g 62 ILE cc_start: 0.9566 (pt) cc_final: 0.9111 (pt) REVERT: g 65 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8932 (mm) REVERT: h 51 ASP cc_start: 0.8561 (p0) cc_final: 0.8308 (p0) REVERT: h 105 GLU cc_start: 0.8506 (tp30) cc_final: 0.8217 (tp30) REVERT: u 53 ARG cc_start: 0.4011 (tpt170) cc_final: 0.3638 (tpt170) outliers start: 10 outliers final: 8 residues processed: 114 average time/residue: 0.1247 time to fit residues: 20.5525 Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3287 r_free = 0.3287 target = 0.036428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.028942 restraints weight = 137025.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.029761 restraints weight = 75496.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.030345 restraints weight = 51719.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.030684 restraints weight = 40171.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.030920 restraints weight = 34443.398| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 14386 Z= 0.379 Angle : 0.772 12.737 20853 Z= 0.440 Chirality : 0.041 0.243 2376 Planarity : 0.005 0.055 1478 Dihedral : 32.361 176.067 4581 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.88 % Allowed : 20.20 % Favored : 77.92 % 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: 0.28 (0.27), residues: 825 helix: 0.64 (0.20), residues: 584 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 131 TYR 0.020 0.003 TYR a 54 PHE 0.012 0.002 PHE g 25 HIS 0.005 0.002 HIS d 49 Details of bonding type rmsd covalent geometry : bond 0.00836 (14386) covalent geometry : angle 0.77192 (20853) hydrogen bonds : bond 0.08228 ( 856) hydrogen bonds : angle 4.09952 ( 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 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 79 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8749 (tptp) REVERT: b 91 LYS cc_start: 0.9398 (ttpp) cc_final: 0.9117 (tttm) REVERT: c 36 LYS cc_start: 0.9063 (mmpt) cc_final: 0.8648 (mmmt) REVERT: c 91 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8495 (tm-30) REVERT: d 102 LEU cc_start: 0.9542 (mm) cc_final: 0.9297 (mp) REVERT: e 97 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7751 (mt-10) REVERT: g 61 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8567 (tm-30) REVERT: g 62 ILE cc_start: 0.9603 (pt) cc_final: 0.9281 (pt) REVERT: u 53 ARG cc_start: 0.4172 (tpt170) cc_final: 0.3730 (tpt170) outliers start: 13 outliers final: 11 residues processed: 105 average time/residue: 0.1165 time to fit residues: 17.6661 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 68 ASP Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.0000 chunk 40 optimal weight: 3.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 63 ASN ** 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 = 0.3381 r_free = 0.3381 target = 0.039463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.032025 restraints weight = 128217.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.032912 restraints weight = 69336.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.033483 restraints weight = 46953.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.033892 restraints weight = 36609.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.034178 restraints weight = 30828.353| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14386 Z= 0.173 Angle : 0.670 11.461 20853 Z= 0.383 Chirality : 0.036 0.190 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.692 176.362 4581 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.15 % Allowed : 21.21 % Favored : 77.63 % 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: 0.75 (0.28), residues: 825 helix: 1.03 (0.21), residues: 586 sheet: -1.47 (1.70), residues: 10 loop : -0.63 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 79 TYR 0.022 0.002 TYR a 54 PHE 0.008 0.001 PHE c 25 HIS 0.002 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00381 (14386) covalent geometry : angle 0.67040 (20853) hydrogen bonds : bond 0.03959 ( 856) hydrogen bonds : angle 3.56979 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.88 seconds wall clock time: 33 minutes 22.31 seconds (2002.31 seconds total)