Starting phenix.real_space_refine on Sat Sep 12 11:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfe_13373/09_2026/7pfe_13373.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfe_13373/09_2026/7pfe_13373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pfe_13373/09_2026/7pfe_13373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfe_13373/09_2026/7pfe_13373.map" model { file = "/net/cci-nas-00/data/ceres_data/7pfe_13373/09_2026/7pfe_13373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfe_13373/09_2026/7pfe_13373.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 354 5.49 5 S 10 5.16 5 C 7617 2.51 5 N 2601 2.21 5 O 3298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13880 Number of models: 1 Model: "" Number of chains: 11 Chain: "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: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3645 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "I" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3612 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} 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: 2.92, per 1000 atoms: 0.21 Number of scatterers: 13880 At special positions: 0 Unit cell: (133.35, 132.3, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 354 15.00 O 3298 8.00 N 2601 7.00 C 7617 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: 1.12 Conformation dependent library (CDL) restraints added in 390.1 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: 39 helices and 10 sheets defined 70.6% alpha, 3.1% beta 174 base pairs and 308 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.783A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.992A 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: 3.716A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 3.542A pdb=" N GLN b 27 " --> pdb=" O ASP b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 74 removed outlier: 4.607A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.205A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.560A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 37 through 49 removed outlier: 3.889A pdb=" N VAL d 41 " --> pdb=" O TYR d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 removed outlier: 3.551A pdb=" N ILE d 94 " --> pdb=" O THR d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.531A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (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 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 4.193A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.547A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.249A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 124 removed outlier: 4.177A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 51 removed outlier: 4.340A pdb=" N LEU u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER u 50 " --> pdb=" O ALA u 46 " (cutoff:3.500A) removed outlier: 3.759A 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: 6.743A 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 Processing sheet with id=AA3, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.347A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (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 'c' and resid 101 through 102 removed outlier: 6.565A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.504A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.226A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'u' and resid 56 through 57 433 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 444 hydrogen bonds 888 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 308 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3118 1.34 - 1.46: 5388 1.46 - 1.58: 5614 1.58 - 1.71: 706 1.71 - 1.83: 20 Bond restraints: 14846 Sorted by residual: bond pdb=" C3' DG I 350 " pdb=" O3' DG I 350 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" C3' DC I 333 " pdb=" O3' DC I 333 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" C5' DA I 342 " pdb=" C4' DA I 342 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.26e+01 bond pdb=" C3' DG J 486 " pdb=" O3' DG J 486 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C3' DT I 330 " pdb=" C2' DT I 330 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 19891 1.93 - 3.85: 1493 3.85 - 5.78: 123 5.78 - 7.71: 41 7.71 - 9.63: 15 Bond angle restraints: 21563 Sorted by residual: angle pdb=" O4' DG I 343 " pdb=" C4' DG I 343 " pdb=" C3' DG I 343 " ideal model delta sigma weight residual 106.00 102.57 3.43 6.00e-01 2.78e+00 3.27e+01 angle pdb=" O4' DA I 363 " pdb=" C4' DA I 363 " pdb=" C3' DA I 363 " ideal model delta sigma weight residual 106.00 102.57 3.43 6.00e-01 2.78e+00 3.27e+01 angle pdb=" N GLU e 94 " pdb=" CA GLU e 94 " pdb=" CB GLU e 94 " ideal model delta sigma weight residual 110.28 118.56 -8.28 1.55e+00 4.16e-01 2.85e+01 angle pdb=" O4' DG J 475 " pdb=" C4' DG J 475 " pdb=" C3' DG J 475 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.79e+01 angle pdb=" O4' DA I 261 " pdb=" C4' DA I 261 " pdb=" C3' DA I 261 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.74e+01 ... (remaining 21558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6170 35.97 - 71.93: 1826 71.93 - 107.90: 25 107.90 - 143.86: 4 143.86 - 179.83: 2 Dihedral angle restraints: 8027 sinusoidal: 5596 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLU b 74 " pdb=" C GLU b 74 " pdb=" N HIS b 75 " pdb=" CA HIS b 75 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ILE b 50 " pdb=" C ILE b 50 " pdb=" N TYR b 51 " pdb=" CA TYR b 51 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LEU a 60 " pdb=" C LEU a 60 " pdb=" N LEU a 61 " pdb=" CA LEU a 61 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 8024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1964 0.065 - 0.129: 431 0.129 - 0.194: 49 0.194 - 0.259: 11 0.259 - 0.323: 1 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CA PHE e 104 " pdb=" N PHE e 104 " pdb=" C PHE e 104 " pdb=" CB PHE e 104 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA GLU a 94 " pdb=" N GLU a 94 " pdb=" C GLU a 94 " pdb=" CB GLU a 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' DG I 350 " pdb=" C4' DG I 350 " pdb=" O3' DG I 350 " pdb=" C2' DG I 350 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2453 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE a 104 " 0.018 2.00e-02 2.50e+03 2.09e-02 7.62e+00 pdb=" CG PHE a 104 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE a 104 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE a 104 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE a 104 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE a 104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE a 104 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE c 79 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO c 80 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO c 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO c 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 99 " 0.214 9.50e-02 1.11e+02 9.63e-02 6.87e+00 pdb=" NE ARG d 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG d 99 " 0.017 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 1495 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3060 2.79 - 3.32: 12862 3.32 - 3.85: 30171 3.85 - 4.37: 33418 4.37 - 4.90: 45752 Nonbonded interactions: 125263 Sorted by model distance: nonbonded pdb=" O GLN e 93 " pdb=" OG SER e 96 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU u 52 " pdb=" OG SER u 54 " model vdw 2.270 3.040 nonbonded pdb=" OG SER c 40 " pdb=" O ARG c 42 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR d 90 " pdb=" OE1 GLU d 93 " model vdw 2.306 3.040 nonbonded pdb=" NE2 HIS a 113 " pdb=" OD1 ASP e 123 " model vdw 2.312 3.120 ... (remaining 125258 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.040 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.008 0.064 14846 Z= 0.655 Angle : 1.069 9.632 21563 Z= 0.837 Chirality : 0.054 0.323 2456 Planarity : 0.008 0.096 1498 Dihedral : 29.754 179.829 6461 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.43 (0.26), residues: 825 helix: 0.09 (0.20), residues: 566 sheet: -2.08 (1.53), residues: 10 loop : -0.80 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG d 99 TYR 0.035 0.003 TYR f 72 PHE 0.048 0.003 PHE a 104 HIS 0.008 0.003 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.66 (14846) covalent geometry : angle 1.06880 / 0.84 (21563) hydrogen bonds : bond 0.11466 / 7.28 ( 877) hydrogen bonds : angle 4.99610 / 3.59 ( 2160) *********************** 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 161 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9307 (mp0) cc_final: 0.9024 (mp0) REVERT: a 81 ASP cc_start: 0.8781 (t0) cc_final: 0.8303 (p0) REVERT: a 94 GLU cc_start: 0.9252 (mp0) cc_final: 0.8561 (mp0) REVERT: c 25 PHE cc_start: 0.8697 (m-80) cc_final: 0.8220 (m-80) REVERT: c 72 ASP cc_start: 0.9478 (m-30) cc_final: 0.9250 (m-30) REVERT: d 85 LYS cc_start: 0.9666 (mppt) cc_final: 0.9451 (mmtm) REVERT: d 99 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8705 (mtp85) REVERT: d 106 LEU cc_start: 0.9478 (mt) cc_final: 0.9174 (mt) REVERT: d 113 GLU cc_start: 0.9130 (mp0) cc_final: 0.8823 (mp0) REVERT: e 50 GLU cc_start: 0.9653 (mp0) cc_final: 0.9278 (mp0) REVERT: e 54 TYR cc_start: 0.9479 (m-80) cc_final: 0.9278 (m-80) REVERT: e 90 MET cc_start: 0.9263 (tpt) cc_final: 0.8975 (tpt) REVERT: e 106 ASP cc_start: 0.9480 (m-30) cc_final: 0.9140 (m-30) REVERT: e 120 MET cc_start: 0.7446 (mtt) cc_final: 0.7055 (mtt) REVERT: e 124 ILE cc_start: 0.9539 (mt) cc_final: 0.9047 (mp) REVERT: f 44 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8998 (ttmt) REVERT: f 85 ASP cc_start: 0.8626 (m-30) cc_final: 0.8339 (m-30) REVERT: g 36 LYS cc_start: 0.9016 (mppt) cc_final: 0.8759 (mmtm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1258 time to fit residues: 29.1999 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 75 HIS d 84 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.030762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.022727 restraints weight = 156058.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.023574 restraints weight = 74654.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.024148 restraints weight = 45948.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.024554 restraints weight = 32583.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.024792 restraints weight = 25252.000| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14846 Z= 0.165 Angle : 0.714 7.370 21563 Z= 0.418 Chirality : 0.047 0.318 2456 Planarity : 0.005 0.060 1498 Dihedral : 33.111 177.164 4809 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.43 % Allowed : 4.76 % Favored : 94.81 % 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: 0.62 (0.27), residues: 825 helix: 0.95 (0.21), residues: 572 sheet: -2.93 (1.19), residues: 10 loop : -0.54 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG a 83 TYR 0.014 0.002 TYR c 39 PHE 0.013 0.001 PHE e 104 HIS 0.004 0.001 HIS h 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.16 (14846) covalent geometry : angle 0.71358 / 0.42 (21563) hydrogen bonds : bond 0.05139 / 3.37 ( 877) hydrogen bonds : angle 3.76997 / 2.69 ( 2160) *********************** 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 149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9313 (mp0) cc_final: 0.8975 (mp0) REVERT: a 59 GLU cc_start: 0.8744 (pm20) cc_final: 0.8434 (pm20) REVERT: a 60 LEU cc_start: 0.8765 (mt) cc_final: 0.8467 (mt) REVERT: a 94 GLU cc_start: 0.9285 (mp0) cc_final: 0.8930 (mm-30) REVERT: c 25 PHE cc_start: 0.8693 (m-80) cc_final: 0.8427 (m-80) REVERT: c 34 LEU cc_start: 0.9599 (mt) cc_final: 0.8904 (pp) REVERT: c 90 ASP cc_start: 0.8618 (t0) cc_final: 0.8371 (t0) REVERT: c 95 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9010 (mppt) REVERT: d 85 LYS cc_start: 0.9703 (mppt) cc_final: 0.9494 (mmtm) REVERT: d 99 ARG cc_start: 0.9060 (ttm110) cc_final: 0.8833 (mtp85) REVERT: e 50 GLU cc_start: 0.9609 (mp0) cc_final: 0.9280 (mp0) REVERT: e 54 TYR cc_start: 0.9445 (m-80) cc_final: 0.9148 (m-80) REVERT: e 90 MET cc_start: 0.9209 (tpt) cc_final: 0.8980 (tpt) REVERT: e 104 PHE cc_start: 0.9618 (m-10) cc_final: 0.9192 (m-80) REVERT: e 106 ASP cc_start: 0.9423 (m-30) cc_final: 0.9155 (m-30) REVERT: f 44 LYS cc_start: 0.9348 (ttmt) cc_final: 0.9090 (ttmt) REVERT: f 85 ASP cc_start: 0.8719 (m-30) cc_final: 0.8395 (m-30) REVERT: g 36 LYS cc_start: 0.8845 (mppt) cc_final: 0.8487 (mmtm) REVERT: g 73 ASN cc_start: 0.9426 (t0) cc_final: 0.9183 (t0) REVERT: h 105 GLU cc_start: 0.9295 (tp30) cc_final: 0.8852 (tp30) outliers start: 3 outliers final: 1 residues processed: 147 average time/residue: 0.1093 time to fit residues: 23.8156 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 60 optimal weight: 0.8980 chunk 104 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN e 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.030127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.022266 restraints weight = 156646.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.023113 restraints weight = 74635.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023696 restraints weight = 45620.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.024060 restraints weight = 31995.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.024325 restraints weight = 24955.616| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14846 Z= 0.176 Angle : 0.699 8.781 21563 Z= 0.407 Chirality : 0.045 0.296 2456 Planarity : 0.005 0.061 1498 Dihedral : 32.960 176.399 4809 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.43 % Allowed : 4.33 % Favored : 95.24 % 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: 0.83 (0.27), residues: 825 helix: 1.11 (0.20), residues: 582 sheet: -2.75 (1.23), residues: 10 loop : -0.57 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 29 TYR 0.024 0.002 TYR f 72 PHE 0.013 0.001 PHE a 104 HIS 0.006 0.002 HIS h 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (14846) covalent geometry : angle 0.69937 / 0.41 (21563) hydrogen bonds : bond 0.06044 / 4.05 ( 877) hydrogen bonds : angle 3.60794 / 2.56 ( 2160) *********************** 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 149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9357 (mp0) cc_final: 0.9049 (mp0) REVERT: a 60 LEU cc_start: 0.8682 (mt) cc_final: 0.8307 (mt) REVERT: a 120 MET cc_start: 0.8794 (mpp) cc_final: 0.8398 (mpp) REVERT: b 62 LEU cc_start: 0.9709 (mm) cc_final: 0.9449 (mt) REVERT: b 74 GLU cc_start: 0.9132 (pm20) cc_final: 0.8651 (pm20) REVERT: c 25 PHE cc_start: 0.8675 (m-80) cc_final: 0.8451 (m-80) REVERT: c 90 ASP cc_start: 0.8726 (t0) cc_final: 0.8238 (t0) REVERT: c 95 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9014 (mppt) REVERT: d 85 LYS cc_start: 0.9707 (mppt) cc_final: 0.9473 (mmtm) REVERT: d 113 GLU cc_start: 0.9076 (mp0) cc_final: 0.8868 (mp0) REVERT: e 50 GLU cc_start: 0.9672 (mp0) cc_final: 0.9386 (mp0) REVERT: e 104 PHE cc_start: 0.9629 (m-10) cc_final: 0.9202 (m-80) REVERT: e 106 ASP cc_start: 0.9447 (m-30) cc_final: 0.9191 (m-30) REVERT: f 44 LYS cc_start: 0.9343 (ttmt) cc_final: 0.9115 (ttmt) REVERT: f 85 ASP cc_start: 0.8613 (m-30) cc_final: 0.8309 (m-30) REVERT: g 73 ASN cc_start: 0.9418 (t0) cc_final: 0.9113 (t0) REVERT: h 68 ASP cc_start: 0.9316 (t0) cc_final: 0.9115 (t0) REVERT: h 105 GLU cc_start: 0.9237 (tp30) cc_final: 0.8936 (tp30) outliers start: 3 outliers final: 3 residues processed: 147 average time/residue: 0.1115 time to fit residues: 24.0355 Evaluate side-chains 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS c 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.029142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.021497 restraints weight = 163648.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.022299 restraints weight = 79660.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.022860 restraints weight = 49238.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.023221 restraints weight = 34840.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.023479 restraints weight = 27323.652| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14846 Z= 0.232 Angle : 0.720 10.107 21563 Z= 0.413 Chirality : 0.045 0.296 2456 Planarity : 0.005 0.061 1498 Dihedral : 33.013 176.295 4809 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 0.87 (0.27), residues: 825 helix: 1.15 (0.20), residues: 582 sheet: -2.60 (1.36), residues: 10 loop : -0.58 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 92 TYR 0.019 0.002 TYR f 98 PHE 0.013 0.002 PHE a 104 HIS 0.007 0.002 HIS a 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.23 (14846) covalent geometry : angle 0.71967 / 0.41 (21563) hydrogen bonds : bond 0.07327 / 4.92 ( 877) hydrogen bonds : angle 3.82529 / 2.71 ( 2160) *********************** 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 137 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9320 (mp0) cc_final: 0.9062 (mp0) REVERT: a 60 LEU cc_start: 0.8634 (mt) cc_final: 0.8318 (mt) REVERT: b 58 LEU cc_start: 0.9835 (tp) cc_final: 0.9465 (pp) REVERT: c 90 ASP cc_start: 0.8663 (t0) cc_final: 0.8187 (t0) REVERT: c 95 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9022 (mppt) REVERT: d 85 LYS cc_start: 0.9703 (mppt) cc_final: 0.9459 (mmtm) REVERT: e 50 GLU cc_start: 0.9662 (mp0) cc_final: 0.9356 (mp0) REVERT: e 104 PHE cc_start: 0.9511 (m-10) cc_final: 0.9171 (m-80) REVERT: e 106 ASP cc_start: 0.9439 (m-30) cc_final: 0.9181 (m-30) REVERT: f 44 LYS cc_start: 0.9373 (ttmt) cc_final: 0.8888 (ttmt) REVERT: f 58 LEU cc_start: 0.9835 (tt) cc_final: 0.9561 (pp) REVERT: f 74 GLU cc_start: 0.9269 (pm20) cc_final: 0.8983 (pm20) REVERT: f 85 ASP cc_start: 0.8731 (m-30) cc_final: 0.8388 (m-30) REVERT: h 71 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8703 (mm-30) REVERT: h 105 GLU cc_start: 0.9166 (tp30) cc_final: 0.8937 (tp30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1124 time to fit residues: 22.8211 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 100 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 27 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.030089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.022111 restraints weight = 159608.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.022924 restraints weight = 77569.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.023498 restraints weight = 47952.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023834 restraints weight = 34111.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.024098 restraints weight = 27048.223| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14846 Z= 0.154 Angle : 0.665 7.822 21563 Z= 0.385 Chirality : 0.044 0.302 2456 Planarity : 0.004 0.057 1498 Dihedral : 32.882 175.809 4809 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.29 % Allowed : 2.60 % Favored : 97.11 % 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: 1.14 (0.27), residues: 825 helix: 1.39 (0.20), residues: 582 sheet: -2.44 (1.48), residues: 10 loop : -0.60 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG c 20 TYR 0.025 0.002 TYR f 72 PHE 0.018 0.001 PHE c 25 HIS 0.005 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (14846) covalent geometry : angle 0.66465 / 0.39 (21563) hydrogen bonds : bond 0.04704 / 3.09 ( 877) hydrogen bonds : angle 3.51958 / 2.49 ( 2160) *********************** 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 151 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9281 (mp0) cc_final: 0.8965 (mp0) REVERT: b 58 LEU cc_start: 0.9824 (tp) cc_final: 0.9445 (pp) REVERT: c 25 PHE cc_start: 0.8630 (m-80) cc_final: 0.8370 (m-80) REVERT: c 34 LEU cc_start: 0.9600 (mt) cc_final: 0.8937 (pp) REVERT: c 90 ASP cc_start: 0.8659 (t0) cc_final: 0.8088 (t0) REVERT: c 91 GLU cc_start: 0.9014 (mp0) cc_final: 0.8752 (mm-30) REVERT: c 95 LYS cc_start: 0.9457 (ttmm) cc_final: 0.8943 (mppt) REVERT: d 85 LYS cc_start: 0.9712 (mppt) cc_final: 0.9454 (mmtm) REVERT: d 99 ARG cc_start: 0.9223 (mtp85) cc_final: 0.8983 (ttm110) REVERT: e 50 GLU cc_start: 0.9663 (mp0) cc_final: 0.9383 (mp0) REVERT: e 82 LEU cc_start: 0.8817 (mt) cc_final: 0.8502 (mt) REVERT: e 104 PHE cc_start: 0.9592 (m-10) cc_final: 0.9120 (m-80) REVERT: e 106 ASP cc_start: 0.9421 (m-30) cc_final: 0.9163 (m-30) REVERT: f 58 LEU cc_start: 0.9825 (tt) cc_final: 0.9534 (pp) REVERT: f 74 GLU cc_start: 0.9201 (pm20) cc_final: 0.8937 (pm20) REVERT: f 85 ASP cc_start: 0.8650 (m-30) cc_final: 0.8321 (m-30) REVERT: f 98 TYR cc_start: 0.8342 (m-10) cc_final: 0.8066 (m-80) REVERT: h 68 ASP cc_start: 0.9300 (t0) cc_final: 0.9075 (t0) REVERT: h 71 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8691 (mm-30) REVERT: h 116 LYS cc_start: 0.9671 (mtmm) cc_final: 0.9419 (ptpp) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.1059 time to fit residues: 23.7470 Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.0670 chunk 36 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN f 75 HIS h 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.030043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.022161 restraints weight = 156618.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.022985 restraints weight = 76545.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.023541 restraints weight = 47544.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.023894 restraints weight = 33863.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.024129 restraints weight = 26722.949| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14846 Z= 0.153 Angle : 0.669 7.897 21563 Z= 0.388 Chirality : 0.044 0.296 2456 Planarity : 0.004 0.056 1498 Dihedral : 32.767 177.103 4809 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.14 % Allowed : 1.15 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.28), residues: 825 helix: 1.40 (0.21), residues: 586 sheet: -2.31 (1.53), residues: 10 loop : -0.70 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 23 TYR 0.015 0.002 TYR h 40 PHE 0.010 0.001 PHE c 25 HIS 0.015 0.002 HIS h 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (14846) covalent geometry : angle 0.66942 / 0.39 (21563) hydrogen bonds : bond 0.04926 / 3.26 ( 877) hydrogen bonds : angle 3.61303 / 2.55 ( 2160) *********************** 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 149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 58 LEU cc_start: 0.9816 (tp) cc_final: 0.9451 (pp) REVERT: c 25 PHE cc_start: 0.8573 (m-80) cc_final: 0.8346 (m-80) REVERT: c 34 LEU cc_start: 0.9598 (mt) cc_final: 0.8943 (pp) REVERT: c 90 ASP cc_start: 0.8681 (t0) cc_final: 0.8103 (t0) REVERT: c 91 GLU cc_start: 0.9007 (mp0) cc_final: 0.8752 (mm-30) REVERT: c 95 LYS cc_start: 0.9449 (ttmm) cc_final: 0.8941 (mppt) REVERT: d 85 LYS cc_start: 0.9715 (mppt) cc_final: 0.9459 (mmtm) REVERT: d 99 ARG cc_start: 0.9262 (mtp85) cc_final: 0.8994 (ttm110) REVERT: e 50 GLU cc_start: 0.9697 (mp0) cc_final: 0.9376 (mp0) REVERT: e 82 LEU cc_start: 0.8829 (mt) cc_final: 0.8476 (mt) REVERT: e 100 LEU cc_start: 0.9587 (mm) cc_final: 0.9175 (mm) REVERT: e 104 PHE cc_start: 0.9452 (m-10) cc_final: 0.9184 (m-80) REVERT: e 105 GLU cc_start: 0.9482 (pm20) cc_final: 0.9235 (pm20) REVERT: e 106 ASP cc_start: 0.9480 (m-30) cc_final: 0.9138 (m-30) REVERT: f 58 LEU cc_start: 0.9819 (tt) cc_final: 0.9422 (pp) REVERT: f 59 LYS cc_start: 0.9831 (ptmm) cc_final: 0.9567 (ptmm) REVERT: f 85 ASP cc_start: 0.8649 (m-30) cc_final: 0.8303 (m-30) REVERT: g 61 GLU cc_start: 0.9493 (tm-30) cc_final: 0.9106 (tm-30) REVERT: h 52 THR cc_start: 0.8174 (m) cc_final: 0.7870 (p) REVERT: h 68 ASP cc_start: 0.9286 (t0) cc_final: 0.9075 (t0) REVERT: h 71 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8684 (mm-30) REVERT: h 116 LYS cc_start: 0.9665 (mtmm) cc_final: 0.9428 (ptpp) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1054 time to fit residues: 23.2249 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN e 108 ASN h 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.029659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.021792 restraints weight = 159034.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.022602 restraints weight = 77617.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.023136 restraints weight = 48195.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023525 restraints weight = 34552.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023767 restraints weight = 27182.177| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14846 Z= 0.176 Angle : 0.674 8.286 21563 Z= 0.389 Chirality : 0.043 0.295 2456 Planarity : 0.004 0.056 1498 Dihedral : 32.720 177.001 4809 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.14 % Allowed : 0.87 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 825 helix: 1.33 (0.21), residues: 586 sheet: -2.08 (1.71), residues: 10 loop : -0.67 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 92 TYR 0.035 0.002 TYR f 98 PHE 0.016 0.002 PHE a 104 HIS 0.006 0.002 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.18 (14846) covalent geometry : angle 0.67422 / 0.39 (21563) hydrogen bonds : bond 0.05629 / 3.75 ( 877) hydrogen bonds : angle 3.64826 / 2.58 ( 2160) *********************** 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 140 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9288 (mp0) cc_final: 0.9026 (mp0) REVERT: c 25 PHE cc_start: 0.8625 (m-80) cc_final: 0.8424 (m-80) REVERT: c 90 ASP cc_start: 0.8692 (t0) cc_final: 0.8096 (t0) REVERT: c 91 GLU cc_start: 0.9017 (mp0) cc_final: 0.8787 (mm-30) REVERT: c 95 LYS cc_start: 0.9439 (ttmm) cc_final: 0.8933 (mppt) REVERT: d 62 MET cc_start: 0.8666 (mmp) cc_final: 0.8414 (mmp) REVERT: d 85 LYS cc_start: 0.9715 (mppt) cc_final: 0.9460 (mmtm) REVERT: d 99 ARG cc_start: 0.9289 (mtp85) cc_final: 0.8996 (ttm110) REVERT: e 60 LEU cc_start: 0.8486 (mp) cc_final: 0.8075 (mt) REVERT: e 82 LEU cc_start: 0.8814 (mt) cc_final: 0.8483 (mt) REVERT: e 104 PHE cc_start: 0.9548 (m-10) cc_final: 0.8955 (m-80) REVERT: e 106 ASP cc_start: 0.9526 (m-30) cc_final: 0.9299 (m-30) REVERT: e 120 MET cc_start: 0.6770 (mtt) cc_final: 0.6408 (mtt) REVERT: f 44 LYS cc_start: 0.9305 (ttmt) cc_final: 0.9031 (ttmt) REVERT: f 58 LEU cc_start: 0.9833 (tt) cc_final: 0.9551 (pp) REVERT: f 85 ASP cc_start: 0.8668 (m-30) cc_final: 0.8301 (m-30) REVERT: g 61 GLU cc_start: 0.9481 (tm-30) cc_final: 0.9071 (tm-30) REVERT: h 52 THR cc_start: 0.8169 (m) cc_final: 0.7777 (p) REVERT: h 68 ASP cc_start: 0.9296 (t0) cc_final: 0.9076 (t0) REVERT: h 71 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8709 (mm-30) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1042 time to fit residues: 22.0615 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN e 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.028366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.020850 restraints weight = 168109.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.021640 restraints weight = 82020.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.022187 restraints weight = 50888.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.022544 restraints weight = 36112.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022755 restraints weight = 28258.970| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14846 Z= 0.254 Angle : 0.736 10.235 21563 Z= 0.417 Chirality : 0.044 0.291 2456 Planarity : 0.005 0.056 1498 Dihedral : 32.860 176.837 4809 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.14 % Allowed : 2.02 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 825 helix: 1.18 (0.20), residues: 582 sheet: -2.15 (1.82), residues: 10 loop : -0.61 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 92 TYR 0.039 0.003 TYR f 98 PHE 0.018 0.002 PHE f 100 HIS 0.009 0.002 HIS a 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.25 (14846) covalent geometry : angle 0.73647 / 0.42 (21563) hydrogen bonds : bond 0.08601 / 5.80 ( 877) hydrogen bonds : angle 3.95454 / 2.79 ( 2160) *********************** 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 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.363 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 50 GLU cc_start: 0.9303 (mp0) cc_final: 0.9008 (mp0) REVERT: a 94 GLU cc_start: 0.9150 (mp0) cc_final: 0.8837 (mp0) REVERT: a 105 GLU cc_start: 0.9145 (mp0) cc_final: 0.8926 (mp0) REVERT: c 25 PHE cc_start: 0.8606 (m-80) cc_final: 0.8338 (m-80) REVERT: c 90 ASP cc_start: 0.8631 (t0) cc_final: 0.8052 (t0) REVERT: c 95 LYS cc_start: 0.9435 (ttmm) cc_final: 0.8986 (mppt) REVERT: d 62 MET cc_start: 0.8688 (mmp) cc_final: 0.8476 (mmp) REVERT: d 99 ARG cc_start: 0.9314 (mtp85) cc_final: 0.8960 (ttm110) REVERT: e 104 PHE cc_start: 0.9547 (m-10) cc_final: 0.9045 (m-80) REVERT: e 106 ASP cc_start: 0.9512 (m-30) cc_final: 0.9003 (m-30) REVERT: e 120 MET cc_start: 0.6489 (mtt) cc_final: 0.6150 (mtt) REVERT: f 58 LEU cc_start: 0.9846 (tt) cc_final: 0.9473 (pp) REVERT: f 85 ASP cc_start: 0.8685 (m-30) cc_final: 0.8323 (m-30) REVERT: g 36 LYS cc_start: 0.8955 (mptt) cc_final: 0.8648 (mmtm) REVERT: g 61 GLU cc_start: 0.9473 (tm-30) cc_final: 0.9057 (tm-30) REVERT: h 71 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8695 (mm-30) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1079 time to fit residues: 20.6203 Evaluate side-chains 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 90 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.028922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.021347 restraints weight = 166144.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.022136 restraints weight = 79758.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.022699 restraints weight = 49150.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023070 restraints weight = 34809.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.023315 restraints weight = 27146.534| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 14846 Z= 0.192 Angle : 0.707 8.593 21563 Z= 0.407 Chirality : 0.044 0.305 2456 Planarity : 0.004 0.052 1498 Dihedral : 32.860 177.587 4809 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.14 % Allowed : 0.87 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.28), residues: 825 helix: 1.10 (0.20), residues: 586 sheet: -2.20 (1.78), residues: 10 loop : -0.67 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 23 TYR 0.044 0.002 TYR f 98 PHE 0.011 0.001 PHE c 25 HIS 0.014 0.002 HIS h 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 (14846) covalent geometry : angle 0.70693 / 0.41 (21563) hydrogen bonds : bond 0.05793 / 3.84 ( 877) hydrogen bonds : angle 3.98871 / 2.84 ( 2160) *********************** 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 135 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9297 (mp0) cc_final: 0.9081 (pm20) REVERT: a 94 GLU cc_start: 0.9112 (mp0) cc_final: 0.8588 (mp0) REVERT: c 25 PHE cc_start: 0.8625 (m-80) cc_final: 0.8366 (m-80) REVERT: c 41 GLU cc_start: 0.8664 (pm20) cc_final: 0.8357 (pm20) REVERT: c 90 ASP cc_start: 0.8513 (t0) cc_final: 0.7993 (t0) REVERT: c 95 LYS cc_start: 0.9467 (ttmm) cc_final: 0.9017 (mppt) REVERT: d 62 MET cc_start: 0.8663 (mmp) cc_final: 0.8435 (mmp) REVERT: d 85 LYS cc_start: 0.9691 (mppt) cc_final: 0.9431 (mmtm) REVERT: d 99 ARG cc_start: 0.9306 (mtp85) cc_final: 0.8945 (ttm110) REVERT: d 113 GLU cc_start: 0.9261 (mp0) cc_final: 0.9050 (mp0) REVERT: e 50 GLU cc_start: 0.9697 (mp0) cc_final: 0.9453 (mp0) REVERT: e 60 LEU cc_start: 0.8496 (mp) cc_final: 0.8096 (mt) REVERT: e 82 LEU cc_start: 0.8843 (mt) cc_final: 0.8517 (mt) REVERT: e 90 MET cc_start: 0.9271 (tpt) cc_final: 0.8925 (tpt) REVERT: e 104 PHE cc_start: 0.9505 (m-10) cc_final: 0.8963 (m-80) REVERT: e 105 GLU cc_start: 0.9559 (pm20) cc_final: 0.9289 (pm20) REVERT: e 106 ASP cc_start: 0.9238 (m-30) cc_final: 0.8986 (m-30) REVERT: e 120 MET cc_start: 0.6655 (mtt) cc_final: 0.6233 (mtt) REVERT: f 53 GLU cc_start: 0.9004 (pt0) cc_final: 0.8775 (pp20) REVERT: f 58 LEU cc_start: 0.9844 (tt) cc_final: 0.9478 (pp) REVERT: f 85 ASP cc_start: 0.8619 (m-30) cc_final: 0.8251 (m-30) REVERT: g 36 LYS cc_start: 0.8931 (mptt) cc_final: 0.8616 (mmtm) REVERT: g 61 GLU cc_start: 0.9479 (tm-30) cc_final: 0.9058 (tm-30) REVERT: h 52 THR cc_start: 0.8292 (m) cc_final: 0.7910 (p) REVERT: h 71 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8702 (mm-30) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1039 time to fit residues: 21.1760 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 0.0060 chunk 98 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.029528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.021578 restraints weight = 165581.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.022346 restraints weight = 82282.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.022884 restraints weight = 51998.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.023236 restraints weight = 37651.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.023481 restraints weight = 30223.266| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14846 Z= 0.168 Angle : 0.696 7.920 21563 Z= 0.403 Chirality : 0.044 0.306 2456 Planarity : 0.004 0.051 1498 Dihedral : 32.742 179.668 4809 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.28), residues: 825 helix: 1.13 (0.21), residues: 584 sheet: -2.29 (1.67), residues: 10 loop : -0.72 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 23 TYR 0.029 0.002 TYR f 98 PHE 0.012 0.001 PHE c 25 HIS 0.011 0.002 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (14846) covalent geometry : angle 0.69572 / 0.40 (21563) hydrogen bonds : bond 0.05127 / 3.38 ( 877) hydrogen bonds : angle 3.93989 / 2.77 ( 2160) ********************** 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 135 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 81 ASP cc_start: 0.9013 (t0) cc_final: 0.8152 (p0) REVERT: a 94 GLU cc_start: 0.9071 (mp0) cc_final: 0.8573 (mp0) REVERT: a 105 GLU cc_start: 0.9130 (mp0) cc_final: 0.8922 (mp0) REVERT: c 25 PHE cc_start: 0.8644 (m-80) cc_final: 0.8363 (m-80) REVERT: c 34 LEU cc_start: 0.9574 (mt) cc_final: 0.8938 (pp) REVERT: c 90 ASP cc_start: 0.8512 (t0) cc_final: 0.7935 (t0) REVERT: c 91 GLU cc_start: 0.8938 (mp0) cc_final: 0.8716 (mm-30) REVERT: c 95 LYS cc_start: 0.9458 (ttmm) cc_final: 0.8954 (mppt) REVERT: d 35 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6307 (mt-10) REVERT: d 62 MET cc_start: 0.8715 (mmp) cc_final: 0.8511 (mmp) REVERT: d 85 LYS cc_start: 0.9686 (mppt) cc_final: 0.9419 (mmtm) REVERT: d 99 ARG cc_start: 0.9273 (mtp85) cc_final: 0.8960 (ttm110) REVERT: d 113 GLU cc_start: 0.9241 (mp0) cc_final: 0.8977 (mp0) REVERT: e 50 GLU cc_start: 0.9638 (mp0) cc_final: 0.9385 (mp0) REVERT: e 60 LEU cc_start: 0.8472 (mp) cc_final: 0.8056 (mt) REVERT: e 79 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9041 (mmmm) REVERT: e 82 LEU cc_start: 0.8922 (mt) cc_final: 0.8575 (mt) REVERT: e 104 PHE cc_start: 0.9464 (m-10) cc_final: 0.8907 (m-80) REVERT: e 105 GLU cc_start: 0.9512 (pm20) cc_final: 0.9249 (pm20) REVERT: e 106 ASP cc_start: 0.9197 (m-30) cc_final: 0.8897 (m-30) REVERT: e 120 MET cc_start: 0.6722 (mtt) cc_final: 0.6323 (mtt) REVERT: f 53 GLU cc_start: 0.9061 (pt0) cc_final: 0.8762 (pp20) REVERT: f 58 LEU cc_start: 0.9827 (tt) cc_final: 0.9462 (pp) REVERT: f 59 LYS cc_start: 0.9830 (ptmm) cc_final: 0.9545 (ptmm) REVERT: f 85 ASP cc_start: 0.8673 (m-30) cc_final: 0.8311 (m-30) REVERT: f 98 TYR cc_start: 0.8329 (m-80) cc_final: 0.7386 (m-10) REVERT: g 61 GLU cc_start: 0.9445 (tm-30) cc_final: 0.9026 (tm-30) REVERT: h 52 THR cc_start: 0.8253 (m) cc_final: 0.7848 (p) REVERT: h 71 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8731 (mm-30) REVERT: h 99 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8136 (mtm180) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1099 time to fit residues: 21.9853 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 100 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 94 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.029179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.021221 restraints weight = 168014.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.022002 restraints weight = 84258.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.022537 restraints weight = 53442.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022897 restraints weight = 38741.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.023152 restraints weight = 30991.884| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14846 Z= 0.193 Angle : 0.708 9.810 21563 Z= 0.405 Chirality : 0.043 0.303 2456 Planarity : 0.005 0.054 1498 Dihedral : 32.726 179.660 4809 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.28), residues: 825 helix: 1.06 (0.20), residues: 584 sheet: -2.26 (1.74), residues: 10 loop : -0.63 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 23 TYR 0.041 0.003 TYR e 99 PHE 0.013 0.002 PHE f 100 HIS 0.010 0.002 HIS h 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.19 (14846) covalent geometry : angle 0.70778 / 0.41 (21563) hydrogen bonds : bond 0.06220 / 4.13 ( 877) hydrogen bonds : angle 3.99504 / 2.81 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.42 seconds wall clock time: 32 minutes 22.69 seconds (1942.69 seconds total)