Starting phenix.real_space_refine on Fri Sep 11 20:56:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fq8_4299/09_2026/6fq8_4299.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fq8_4299/09_2026/6fq8_4299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6fq8_4299/09_2026/6fq8_4299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fq8_4299/09_2026/6fq8_4299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6fq8_4299/09_2026/6fq8_4299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fq8_4299/09_2026/6fq8_4299.map" } resolution = 4.8 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= 0.003 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 294 5.49 5 S 12 5.16 5 C 6575 2.51 5 N 2231 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 11913 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 765 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} 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: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 3.16, per 1000 atoms: 0.27 Number of scatterers: 11913 At special positions: 0 Unit cell: (77, 123.2, 110.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 294 15.00 O 2801 8.00 N 2231 7.00 C 6575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 361.9 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 75.1% alpha, 2.7% beta 145 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.625A 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 47 through 77 removed outlier: 4.170A pdb=" N TYR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.563A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.374A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.726A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.841A 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.678A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.513A 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 removed outlier: 3.845A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.687A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.011A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.586A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 4.020A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.346A 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 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.968A 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: 3.653A 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 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.050A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.439A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.007A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.817A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 404 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.35 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: 1837 1.33 - 1.45: 4571 1.45 - 1.57: 5708 1.57 - 1.69: 586 1.69 - 1.81: 22 Bond restraints: 12724 Sorted by residual: bond pdb=" C3' DT J 34 " pdb=" O3' DT J 34 " ideal model delta sigma weight residual 1.435 1.358 0.077 1.30e-02 5.92e+03 3.48e+01 bond pdb=" C3' DC J 37 " pdb=" O3' DC J 37 " ideal model delta sigma weight residual 1.435 1.362 0.073 1.30e-02 5.92e+03 3.15e+01 bond pdb=" C5' DC J 10 " pdb=" C4' DC J 10 " ideal model delta sigma weight residual 1.512 1.474 0.038 7.00e-03 2.04e+04 2.89e+01 bond pdb=" C5' DA I 26 " pdb=" C4' DA I 26 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.72e+01 bond pdb=" C5' DA I -15 " pdb=" C4' DA I -15 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.58e+01 ... (remaining 12719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 17785 2.93 - 5.86: 615 5.86 - 8.79: 47 8.79 - 11.72: 6 11.72 - 14.65: 1 Bond angle restraints: 18454 Sorted by residual: angle pdb=" O4' DA I 26 " pdb=" C1' DA I 26 " pdb=" N9 DA I 26 " ideal model delta sigma weight residual 108.00 100.85 7.15 7.00e-01 2.04e+00 1.04e+02 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 114.44 -6.44 7.00e-01 2.04e+00 8.46e+01 angle pdb=" O4' DG I 20 " pdb=" C1' DG I 20 " pdb=" N9 DG I 20 " ideal model delta sigma weight residual 108.00 114.41 -6.41 7.00e-01 2.04e+00 8.38e+01 angle pdb=" O4' DC I -26 " pdb=" C1' DC I -26 " pdb=" N1 DC I -26 " ideal model delta sigma weight residual 108.00 101.77 6.23 7.00e-01 2.04e+00 7.91e+01 angle pdb=" O4' DA I -15 " pdb=" C1' DA I -15 " pdb=" N9 DA I -15 " ideal model delta sigma weight residual 108.00 102.57 5.43 7.00e-01 2.04e+00 6.01e+01 ... (remaining 18449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.58: 5446 32.58 - 65.15: 1398 65.15 - 97.73: 37 97.73 - 130.30: 4 130.30 - 162.88: 2 Dihedral angle restraints: 6887 sinusoidal: 4725 harmonic: 2162 Sorted by residual: dihedral pdb=" CA VAL B 21 " pdb=" C VAL B 21 " pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 57.12 162.88 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 59.56 160.44 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1446 0.073 - 0.145: 552 0.145 - 0.218: 99 0.218 - 0.290: 9 0.290 - 0.363: 4 Chirality restraints: 2110 Sorted by residual: chirality pdb=" C1' DG I 20 " pdb=" O4' DG I 20 " pdb=" C2' DG I 20 " pdb=" N9 DG I 20 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C1' DA J 16 " pdb=" O4' DA J 16 " pdb=" C2' DA J 16 " pdb=" N9 DA J 16 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C1' DG J -40 " pdb=" O4' DG J -40 " pdb=" C2' DG J -40 " pdb=" N9 DG J -40 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2107 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 54 " 0.061 2.00e-02 2.50e+03 2.88e-02 2.07e+01 pdb=" N1 DT I 54 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DT I 54 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DT I 54 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT I 54 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DT I 54 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT I 54 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DT I 54 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 54 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 54 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.065 2.00e-02 2.50e+03 2.71e-02 2.02e+01 pdb=" N9 DA I 26 " 0.048 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.019 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.028 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -15 " 0.062 2.00e-02 2.50e+03 2.67e-02 1.96e+01 pdb=" N9 DA I -15 " -0.054 2.00e-02 2.50e+03 pdb=" C8 DA I -15 " -0.012 2.00e-02 2.50e+03 pdb=" N7 DA I -15 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA I -15 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA I -15 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -15 " 0.025 2.00e-02 2.50e+03 pdb=" N1 DA I -15 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I -15 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DA I -15 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA I -15 " -0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2096 2.78 - 3.31: 11080 3.31 - 3.84: 25147 3.84 - 4.37: 28356 4.37 - 4.90: 39116 Nonbonded interactions: 105795 Sorted by model distance: nonbonded pdb=" OH TYR H 39 " pdb=" OP2 DG J -52 " model vdw 2.252 3.040 nonbonded pdb=" O2 DC I 61 " pdb=" N2 DG J -61 " model vdw 2.256 2.496 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.277 3.040 nonbonded pdb=" O ILE B 50 " pdb=" OG1 THR B 54 " model vdw 2.278 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.320 3.040 ... (remaining 105790 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' and resid 40 through 132) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 100) selection = (chain 'F' and resid 20 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 117) } 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 : 0.009 0.077 12724 Z= 0.839 Angle : 1.255 14.650 18454 Z= 0.977 Chirality : 0.074 0.363 2110 Planarity : 0.008 0.041 1313 Dihedral : 26.946 162.875 5491 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.27), residues: 728 helix: -0.24 (0.20), residues: 502 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 45 TYR 0.034 0.003 TYR A 41 PHE 0.044 0.005 PHE A 104 HIS 0.015 0.003 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00923 / 0.84 (12724) covalent geometry : angle 1.25543 / 0.98 (18454) hydrogen bonds : bond 0.13949 / 9.18 ( 774) hydrogen bonds : angle 6.31798 / 4.54 ( 1921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.322 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: 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: 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 93 GLN cc_start: 0.8961 (tt0) cc_final: 0.8093 (tp-100) REVERT: A 94 GLU cc_start: 0.9089 (tp30) cc_final: 0.8883 (tm-30) REVERT: A 97 GLU cc_start: 0.8654 (mt-10) cc_final: 0.7332 (mt-10) REVERT: A 100 LEU cc_start: 0.9661 (mt) cc_final: 0.9356 (pp) REVERT: B 63 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 84 MET cc_start: 0.9144 (mmt) cc_final: 0.8799 (mpp) REVERT: C 38 ASN cc_start: 0.7504 (m-40) cc_final: 0.7170 (m-40) REVERT: C 64 GLU cc_start: 0.9468 (tt0) cc_final: 0.9214 (tp30) REVERT: C 92 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8912 (pt0) REVERT: D 54 LYS cc_start: 0.9408 (mttt) cc_final: 0.9088 (tmtt) REVERT: D 99 LEU cc_start: 0.9593 (mt) cc_final: 0.9325 (tp) REVERT: E 110 CYS cc_start: 0.8827 (m) cc_final: 0.8215 (m) REVERT: E 124 ILE cc_start: 0.9503 (mt) cc_final: 0.9266 (mp) REVERT: F 62 LEU cc_start: 0.9610 (mt) cc_final: 0.9192 (pp) REVERT: F 68 ASP cc_start: 0.9423 (m-30) cc_final: 0.9171 (m-30) REVERT: F 72 TYR cc_start: 0.9186 (m-80) cc_final: 0.8859 (m-80) REVERT: F 81 VAL cc_start: 0.8490 (t) cc_final: 0.8281 (t) REVERT: F 84 MET cc_start: 0.8590 (mmm) cc_final: 0.7665 (ttp) REVERT: G 34 LEU cc_start: 0.9500 (mt) cc_final: 0.9242 (mt) REVERT: G 36 LYS cc_start: 0.9543 (mttm) cc_final: 0.9326 (mmtm) REVERT: G 38 ASN cc_start: 0.7501 (m110) cc_final: 0.6341 (t0) REVERT: G 84 GLN cc_start: 0.8676 (tp40) cc_final: 0.8196 (tm-30) REVERT: G 94 ASN cc_start: 0.8078 (t0) cc_final: 0.7819 (t0) REVERT: H 54 LYS cc_start: 0.9309 (tptm) cc_final: 0.8977 (tptt) REVERT: H 59 MET cc_start: 0.9382 (mmm) cc_final: 0.8791 (mmm) REVERT: H 65 ASP cc_start: 0.8494 (t0) cc_final: 0.8262 (t70) REVERT: H 66 VAL cc_start: 0.8933 (t) cc_final: 0.8701 (m) REVERT: H 81 ASN cc_start: 0.9315 (m-40) cc_final: 0.8922 (p0) REVERT: H 100 PRO cc_start: 0.8731 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: H 103 LEU cc_start: 0.8697 (mt) cc_final: 0.8480 (mt) REVERT: H 106 HIS cc_start: 0.9397 (m-70) cc_final: 0.9028 (m-70) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1433 time to fit residues: 42.6020 Evaluate side-chains 138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN D 46 HIS E 68 GLN E 85 GLN F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.051915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045410 restraints weight = 142239.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.046825 restraints weight = 87687.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.047872 restraints weight = 60012.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.048651 restraints weight = 42827.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.049241 restraints weight = 31701.227| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12724 Z= 0.211 Angle : 0.868 9.386 18454 Z= 0.488 Chirality : 0.056 0.397 2110 Planarity : 0.006 0.046 1313 Dihedral : 31.805 179.318 4038 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % 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: 0.10 (0.29), residues: 728 helix: 0.60 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 45 TYR 0.035 0.003 TYR A 54 PHE 0.023 0.003 PHE C 25 HIS 0.005 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.21 (12724) covalent geometry : angle 0.86803 / 0.49 (18454) hydrogen bonds : bond 0.09169 / 6.16 ( 774) hydrogen bonds : angle 4.47479 / 3.23 ( 1921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.325 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8950 (mt) cc_final: 0.8714 (mt) REVERT: A 100 LEU cc_start: 0.9805 (mt) cc_final: 0.9504 (mt) REVERT: B 62 LEU cc_start: 0.9523 (mm) cc_final: 0.9223 (mm) REVERT: B 63 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 84 MET cc_start: 0.9232 (mmt) cc_final: 0.8927 (mpp) REVERT: B 97 LEU cc_start: 0.8842 (tp) cc_final: 0.8134 (tp) REVERT: C 38 ASN cc_start: 0.7486 (m-40) cc_final: 0.7247 (m-40) REVERT: C 64 GLU cc_start: 0.9448 (tt0) cc_final: 0.9212 (tp30) REVERT: C 68 ASN cc_start: 0.9335 (m-40) cc_final: 0.9081 (m110) REVERT: D 54 LYS cc_start: 0.9522 (mttt) cc_final: 0.9184 (tmtt) REVERT: D 99 LEU cc_start: 0.9519 (mt) cc_final: 0.9223 (tp) REVERT: E 110 CYS cc_start: 0.9085 (m) cc_final: 0.8487 (m) REVERT: F 62 LEU cc_start: 0.9653 (mt) cc_final: 0.9427 (pp) REVERT: F 68 ASP cc_start: 0.9599 (m-30) cc_final: 0.9222 (m-30) REVERT: F 72 TYR cc_start: 0.9320 (m-80) cc_final: 0.8934 (m-80) REVERT: F 84 MET cc_start: 0.8027 (mmm) cc_final: 0.7319 (ttp) REVERT: G 38 ASN cc_start: 0.7673 (m110) cc_final: 0.6470 (t0) REVERT: G 84 GLN cc_start: 0.8258 (tp40) cc_final: 0.7654 (tm-30) REVERT: G 94 ASN cc_start: 0.7876 (t0) cc_final: 0.7555 (t0) REVERT: H 54 LYS cc_start: 0.9135 (tptm) cc_final: 0.8832 (tptt) REVERT: H 59 MET cc_start: 0.9496 (mmm) cc_final: 0.8983 (mmm) REVERT: H 81 ASN cc_start: 0.9076 (m-40) cc_final: 0.8749 (t0) REVERT: H 100 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.7905 (Cg_endo) REVERT: H 103 LEU cc_start: 0.9030 (mt) cc_final: 0.8488 (mt) REVERT: H 106 HIS cc_start: 0.9700 (m-70) cc_final: 0.9313 (m-70) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1255 time to fit residues: 29.7295 Evaluate side-chains 120 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 chunk 84 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 17 optimal weight: 0.0770 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 64 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.050385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044080 restraints weight = 146427.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.045532 restraints weight = 89297.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.046499 restraints weight = 59581.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.047220 restraints weight = 42748.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.047804 restraints weight = 32024.979| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12724 Z= 0.218 Angle : 0.828 14.008 18454 Z= 0.467 Chirality : 0.054 0.448 2110 Planarity : 0.006 0.048 1313 Dihedral : 32.210 177.246 4038 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % 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: 0.01 (0.28), residues: 728 helix: 0.57 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.033 0.003 TYR G 57 PHE 0.023 0.003 PHE A 104 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.22 (12724) covalent geometry : angle 0.82820 / 0.47 (18454) hydrogen bonds : bond 0.09582 / 6.43 ( 774) hydrogen bonds : angle 4.32632 / 3.13 ( 1921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.307 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: 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: symmetry clash REVERT: A 100 LEU cc_start: 0.9789 (mt) cc_final: 0.9490 (mt) REVERT: A 104 PHE cc_start: 0.9565 (m-80) cc_final: 0.9306 (m-80) REVERT: B 53 GLU cc_start: 0.9416 (tp30) cc_final: 0.9148 (tp30) REVERT: B 63 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 84 MET cc_start: 0.9236 (mmt) cc_final: 0.8908 (mpp) REVERT: C 64 GLU cc_start: 0.9458 (tt0) cc_final: 0.9211 (tp30) REVERT: C 68 ASN cc_start: 0.9334 (m-40) cc_final: 0.9083 (m110) REVERT: D 54 LYS cc_start: 0.9508 (mttt) cc_final: 0.9188 (tmtt) REVERT: D 99 LEU cc_start: 0.9450 (mt) cc_final: 0.9127 (tp) REVERT: E 92 LEU cc_start: 0.8693 (mt) cc_final: 0.8470 (mt) REVERT: E 110 CYS cc_start: 0.9029 (m) cc_final: 0.8332 (m) REVERT: F 62 LEU cc_start: 0.9738 (mt) cc_final: 0.9435 (pp) REVERT: F 72 TYR cc_start: 0.9354 (m-80) cc_final: 0.8685 (m-80) REVERT: F 74 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: G 38 ASN cc_start: 0.7935 (m110) cc_final: 0.7238 (t0) REVERT: G 57 TYR cc_start: 0.9124 (t80) cc_final: 0.8609 (t80) REVERT: G 84 GLN cc_start: 0.8126 (tp40) cc_final: 0.7541 (tm-30) REVERT: G 94 ASN cc_start: 0.7913 (t0) cc_final: 0.7614 (m-40) REVERT: G 102 ILE cc_start: 0.7164 (tt) cc_final: 0.6900 (tt) REVERT: H 54 LYS cc_start: 0.9136 (tptm) cc_final: 0.8844 (tptt) REVERT: H 59 MET cc_start: 0.9372 (mmm) cc_final: 0.8974 (mmm) REVERT: H 81 ASN cc_start: 0.9028 (m110) cc_final: 0.8707 (p0) REVERT: H 100 PRO cc_start: 0.8301 (Cg_exo) cc_final: 0.7878 (Cg_endo) REVERT: H 103 LEU cc_start: 0.8945 (mt) cc_final: 0.8582 (mt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1294 time to fit residues: 27.3486 Evaluate side-chains 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 50.0000 chunk 22 optimal weight: 9.9990 chunk 83 optimal weight: 50.0000 chunk 68 optimal weight: 8.9990 chunk 87 optimal weight: 50.0000 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.050211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043907 restraints weight = 144158.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.045286 restraints weight = 87697.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.046294 restraints weight = 59493.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.047040 restraints weight = 42536.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.047600 restraints weight = 31534.250| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12724 Z= 0.190 Angle : 0.769 13.548 18454 Z= 0.439 Chirality : 0.051 0.437 2110 Planarity : 0.006 0.057 1313 Dihedral : 32.362 179.308 4038 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 0.35 (0.29), residues: 728 helix: 0.82 (0.21), residues: 529 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.016 0.002 TYR G 50 PHE 0.022 0.003 PHE A 104 HIS 0.009 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.19 (12724) covalent geometry : angle 0.76924 / 0.44 (18454) hydrogen bonds : bond 0.08198 / 5.51 ( 774) hydrogen bonds : angle 4.08426 / 2.96 ( 1921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9100 (pt0) cc_final: 0.8590 (pt0) REVERT: A 100 LEU cc_start: 0.9796 (mt) cc_final: 0.9470 (mt) REVERT: B 59 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9299 (mttt) REVERT: B 62 LEU cc_start: 0.9522 (mm) cc_final: 0.9317 (mm) REVERT: B 63 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 68 ASP cc_start: 0.9541 (m-30) cc_final: 0.9340 (m-30) REVERT: B 84 MET cc_start: 0.9193 (mmt) cc_final: 0.8859 (mpp) REVERT: C 38 ASN cc_start: 0.7581 (m-40) cc_final: 0.7221 (t0) REVERT: C 64 GLU cc_start: 0.9476 (tt0) cc_final: 0.9225 (tp30) REVERT: C 68 ASN cc_start: 0.9318 (m-40) cc_final: 0.9046 (m110) REVERT: D 54 LYS cc_start: 0.9517 (mttt) cc_final: 0.9156 (tmtt) REVERT: D 99 LEU cc_start: 0.9435 (mt) cc_final: 0.9104 (tp) REVERT: E 92 LEU cc_start: 0.8702 (mt) cc_final: 0.8476 (mt) REVERT: E 110 CYS cc_start: 0.9026 (m) cc_final: 0.8114 (m) REVERT: F 62 LEU cc_start: 0.9724 (mt) cc_final: 0.9449 (pp) REVERT: F 72 TYR cc_start: 0.9271 (m-80) cc_final: 0.8644 (m-80) REVERT: F 84 MET cc_start: 0.7900 (mmm) cc_final: 0.7155 (ttp) REVERT: G 38 ASN cc_start: 0.8062 (m110) cc_final: 0.7269 (t0) REVERT: G 57 TYR cc_start: 0.8936 (t80) cc_final: 0.8291 (t80) REVERT: G 84 GLN cc_start: 0.8062 (tp40) cc_final: 0.7483 (tm-30) REVERT: G 94 ASN cc_start: 0.7869 (t0) cc_final: 0.7545 (m-40) REVERT: H 54 LYS cc_start: 0.9150 (tptm) cc_final: 0.8850 (tptt) REVERT: H 59 MET cc_start: 0.9392 (mmm) cc_final: 0.8973 (mmm) REVERT: H 81 ASN cc_start: 0.8935 (m110) cc_final: 0.8629 (p0) REVERT: H 100 PRO cc_start: 0.8217 (Cg_exo) cc_final: 0.7824 (Cg_endo) REVERT: H 103 LEU cc_start: 0.8807 (mt) cc_final: 0.8268 (mt) REVERT: H 106 HIS cc_start: 0.9290 (t70) cc_final: 0.8497 (t70) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1383 time to fit residues: 27.9846 Evaluate side-chains 114 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 8.9990 chunk 63 optimal weight: 30.0000 chunk 88 optimal weight: 50.0000 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 93 optimal weight: 50.0000 chunk 43 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.046021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.039321 restraints weight = 144751.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.040663 restraints weight = 91092.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.041609 restraints weight = 62659.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.042274 restraints weight = 45776.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.042752 restraints weight = 35260.310| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12724 Z= 0.198 Angle : 0.766 13.293 18454 Z= 0.436 Chirality : 0.050 0.426 2110 Planarity : 0.006 0.086 1313 Dihedral : 32.392 179.426 4038 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 0.52 (0.29), residues: 728 helix: 1.02 (0.21), residues: 529 sheet: None (None), residues: 0 loop : -1.39 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 116 TYR 0.021 0.002 TYR H 37 PHE 0.022 0.002 PHE F 61 HIS 0.005 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.20 (12724) covalent geometry : angle 0.76618 / 0.44 (18454) hydrogen bonds : bond 0.09095 / 6.10 ( 774) hydrogen bonds : angle 4.05555 / 2.96 ( 1921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9122 (pt0) cc_final: 0.8630 (pt0) REVERT: A 100 LEU cc_start: 0.9802 (mt) cc_final: 0.9481 (mt) REVERT: B 59 LYS cc_start: 0.9495 (mtmm) cc_final: 0.9288 (mttt) REVERT: B 62 LEU cc_start: 0.9527 (mm) cc_final: 0.9316 (mm) REVERT: B 63 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7923 (mt-10) REVERT: B 68 ASP cc_start: 0.9616 (m-30) cc_final: 0.9341 (m-30) REVERT: B 84 MET cc_start: 0.9189 (mmt) cc_final: 0.8802 (mpp) REVERT: C 38 ASN cc_start: 0.7644 (m-40) cc_final: 0.7352 (t0) REVERT: C 64 GLU cc_start: 0.9437 (tt0) cc_final: 0.9185 (tp30) REVERT: C 68 ASN cc_start: 0.9291 (m-40) cc_final: 0.9036 (m110) REVERT: D 54 LYS cc_start: 0.9527 (mttt) cc_final: 0.9203 (tmtt) REVERT: D 99 LEU cc_start: 0.9415 (mt) cc_final: 0.9044 (tp) REVERT: E 92 LEU cc_start: 0.8697 (mt) cc_final: 0.8463 (mt) REVERT: E 94 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8907 (mm-30) REVERT: F 62 LEU cc_start: 0.9738 (mt) cc_final: 0.9472 (pp) REVERT: F 72 TYR cc_start: 0.9298 (m-80) cc_final: 0.8660 (m-80) REVERT: F 84 MET cc_start: 0.8015 (mmm) cc_final: 0.7204 (ttp) REVERT: G 34 LEU cc_start: 0.9469 (mt) cc_final: 0.9256 (mt) REVERT: G 35 ARG cc_start: 0.9528 (mtm180) cc_final: 0.9306 (mmm-85) REVERT: G 38 ASN cc_start: 0.8072 (m110) cc_final: 0.7319 (t0) REVERT: G 57 TYR cc_start: 0.8788 (t80) cc_final: 0.8293 (t80) REVERT: G 84 GLN cc_start: 0.8251 (tp40) cc_final: 0.7743 (tm-30) REVERT: G 94 ASN cc_start: 0.8018 (t0) cc_final: 0.7692 (m-40) REVERT: H 37 TYR cc_start: 0.7424 (m-80) cc_final: 0.6637 (m-10) REVERT: H 54 LYS cc_start: 0.9152 (tptm) cc_final: 0.8823 (tptt) REVERT: H 59 MET cc_start: 0.9457 (mmm) cc_final: 0.8998 (mmm) REVERT: H 81 ASN cc_start: 0.8954 (m110) cc_final: 0.8712 (p0) REVERT: H 100 PRO cc_start: 0.8292 (Cg_exo) cc_final: 0.7908 (Cg_endo) REVERT: H 103 LEU cc_start: 0.8864 (mt) cc_final: 0.8288 (mt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1316 time to fit residues: 26.4891 Evaluate side-chains 113 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 chunk 13 optimal weight: 0.0870 chunk 43 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 chunk 90 optimal weight: 50.0000 chunk 23 optimal weight: 10.0000 overall best weight: 5.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.045772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039123 restraints weight = 144875.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040464 restraints weight = 91090.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.041400 restraints weight = 62404.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.042075 restraints weight = 45603.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.042591 restraints weight = 34990.413| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12724 Z= 0.193 Angle : 0.756 13.122 18454 Z= 0.432 Chirality : 0.049 0.423 2110 Planarity : 0.006 0.082 1313 Dihedral : 32.482 179.859 4038 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 0.52 (0.29), residues: 728 helix: 1.04 (0.21), residues: 529 sheet: None (None), residues: 0 loop : -1.46 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 96 TYR 0.024 0.002 TYR B 72 PHE 0.038 0.003 PHE A 104 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.19 (12724) covalent geometry : angle 0.75632 / 0.43 (18454) hydrogen bonds : bond 0.08680 / 5.80 ( 774) hydrogen bonds : angle 4.04561 / 2.96 ( 1921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.194 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: 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 97 GLU cc_start: 0.9229 (pt0) cc_final: 0.8725 (pt0) REVERT: A 120 MET cc_start: 0.9419 (mtt) cc_final: 0.9135 (mtp) REVERT: B 59 LYS cc_start: 0.9509 (mtmm) cc_final: 0.9309 (mttt) REVERT: B 62 LEU cc_start: 0.9535 (mm) cc_final: 0.9329 (mm) REVERT: B 63 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 68 ASP cc_start: 0.9622 (m-30) cc_final: 0.9367 (m-30) REVERT: B 84 MET cc_start: 0.9185 (mmt) cc_final: 0.8801 (mpp) REVERT: C 64 GLU cc_start: 0.9439 (tt0) cc_final: 0.9190 (tp30) REVERT: C 68 ASN cc_start: 0.9296 (m-40) cc_final: 0.9050 (m110) REVERT: D 99 LEU cc_start: 0.9413 (mt) cc_final: 0.9008 (tp) REVERT: E 92 LEU cc_start: 0.8712 (mt) cc_final: 0.8450 (mt) REVERT: E 94 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8891 (mm-30) REVERT: E 110 CYS cc_start: 0.8663 (m) cc_final: 0.8433 (m) REVERT: F 62 LEU cc_start: 0.9722 (mt) cc_final: 0.9462 (pp) REVERT: F 72 TYR cc_start: 0.9267 (m-80) cc_final: 0.8735 (m-80) REVERT: F 84 MET cc_start: 0.8101 (mmm) cc_final: 0.7227 (ttp) REVERT: G 84 GLN cc_start: 0.8132 (tp40) cc_final: 0.7573 (tm-30) REVERT: G 94 ASN cc_start: 0.8083 (t0) cc_final: 0.7781 (m-40) REVERT: H 37 TYR cc_start: 0.7593 (m-80) cc_final: 0.6772 (m-10) REVERT: H 54 LYS cc_start: 0.9139 (tptm) cc_final: 0.8813 (tptt) REVERT: H 59 MET cc_start: 0.9468 (mmm) cc_final: 0.9008 (mmm) REVERT: H 100 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8114 (Cg_endo) REVERT: H 103 LEU cc_start: 0.8824 (mt) cc_final: 0.8223 (mt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1365 time to fit residues: 26.2409 Evaluate side-chains 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 40.0000 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 80 optimal weight: 50.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.049358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.043273 restraints weight = 145433.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.044666 restraints weight = 88569.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.045632 restraints weight = 59035.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.046370 restraints weight = 42300.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.046909 restraints weight = 31390.399| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12724 Z= 0.176 Angle : 0.734 14.058 18454 Z= 0.421 Chirality : 0.049 0.415 2110 Planarity : 0.006 0.067 1313 Dihedral : 32.542 179.974 4038 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 0.53 (0.29), residues: 728 helix: 1.04 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.45 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 96 TYR 0.015 0.002 TYR H 37 PHE 0.023 0.002 PHE F 61 HIS 0.008 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.18 (12724) covalent geometry : angle 0.73385 / 0.42 (18454) hydrogen bonds : bond 0.07653 / 5.11 ( 774) hydrogen bonds : angle 3.96483 / 2.90 ( 1921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.309 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: 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 97 GLU cc_start: 0.9153 (pt0) cc_final: 0.8673 (pt0) REVERT: A 100 LEU cc_start: 0.9818 (mt) cc_final: 0.9452 (mt) REVERT: A 120 MET cc_start: 0.9434 (mtt) cc_final: 0.9074 (mtp) REVERT: B 62 LEU cc_start: 0.9562 (mm) cc_final: 0.9336 (mm) REVERT: B 63 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 68 ASP cc_start: 0.9632 (m-30) cc_final: 0.9323 (m-30) REVERT: B 84 MET cc_start: 0.9158 (mmt) cc_final: 0.8779 (mpp) REVERT: C 64 GLU cc_start: 0.9498 (tt0) cc_final: 0.9211 (tp30) REVERT: C 68 ASN cc_start: 0.9316 (m-40) cc_final: 0.9072 (m110) REVERT: D 54 LYS cc_start: 0.9528 (mttt) cc_final: 0.9244 (tmtt) REVERT: D 99 LEU cc_start: 0.9375 (mt) cc_final: 0.9010 (tp) REVERT: E 81 ASP cc_start: 0.6919 (t0) cc_final: 0.6080 (m-30) REVERT: E 92 LEU cc_start: 0.8713 (mt) cc_final: 0.8497 (mt) REVERT: E 94 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8878 (mm-30) REVERT: E 110 CYS cc_start: 0.8714 (m) cc_final: 0.8393 (m) REVERT: F 62 LEU cc_start: 0.9736 (mt) cc_final: 0.9454 (pp) REVERT: F 72 TYR cc_start: 0.9309 (m-80) cc_final: 0.8726 (m-80) REVERT: F 84 MET cc_start: 0.8124 (mmm) cc_final: 0.7228 (ttp) REVERT: G 57 TYR cc_start: 0.8755 (t80) cc_final: 0.8552 (t80) REVERT: G 84 GLN cc_start: 0.8000 (tp40) cc_final: 0.7443 (tm-30) REVERT: G 94 ASN cc_start: 0.8001 (t0) cc_final: 0.7691 (m-40) REVERT: H 59 MET cc_start: 0.9512 (mmm) cc_final: 0.9118 (mmm) REVERT: H 100 PRO cc_start: 0.8438 (Cg_exo) cc_final: 0.8078 (Cg_endo) REVERT: H 103 LEU cc_start: 0.8556 (mt) cc_final: 0.8138 (mt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1329 time to fit residues: 25.7046 Evaluate side-chains 106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 40.0000 chunk 17 optimal weight: 0.0040 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 40.0000 chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.049442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.043018 restraints weight = 151561.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.044439 restraints weight = 93965.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.045434 restraints weight = 63652.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.046160 restraints weight = 45687.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.046728 restraints weight = 34460.721| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12724 Z= 0.163 Angle : 0.736 13.635 18454 Z= 0.419 Chirality : 0.049 0.408 2110 Planarity : 0.007 0.159 1313 Dihedral : 32.566 179.626 4038 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % 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: 0.75 (0.30), residues: 728 helix: 1.25 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.43 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 96 TYR 0.028 0.002 TYR B 72 PHE 0.023 0.002 PHE F 61 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (12724) covalent geometry : angle 0.73596 / 0.42 (18454) hydrogen bonds : bond 0.06974 / 4.62 ( 774) hydrogen bonds : angle 3.92739 / 2.88 ( 1921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 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: 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 97 GLU cc_start: 0.9207 (pt0) cc_final: 0.8748 (pt0) REVERT: A 120 MET cc_start: 0.9455 (mtt) cc_final: 0.9204 (mtt) REVERT: B 62 LEU cc_start: 0.9597 (mm) cc_final: 0.9397 (mm) REVERT: B 68 ASP cc_start: 0.9638 (m-30) cc_final: 0.9359 (m-30) REVERT: B 84 MET cc_start: 0.9179 (mmt) cc_final: 0.8860 (mpp) REVERT: C 64 GLU cc_start: 0.9523 (tt0) cc_final: 0.9238 (tp30) REVERT: C 68 ASN cc_start: 0.9329 (m-40) cc_final: 0.9087 (m110) REVERT: D 54 LYS cc_start: 0.9496 (mttt) cc_final: 0.9117 (tptt) REVERT: E 81 ASP cc_start: 0.7045 (t0) cc_final: 0.6235 (m-30) REVERT: E 94 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8868 (mm-30) REVERT: E 106 ASP cc_start: 0.9533 (t0) cc_final: 0.9304 (t0) REVERT: E 110 CYS cc_start: 0.8784 (m) cc_final: 0.8461 (m) REVERT: F 62 LEU cc_start: 0.9734 (mt) cc_final: 0.9471 (pp) REVERT: F 72 TYR cc_start: 0.9379 (m-80) cc_final: 0.8774 (m-80) REVERT: F 84 MET cc_start: 0.8142 (mmm) cc_final: 0.7252 (ttp) REVERT: G 94 ASN cc_start: 0.7788 (t0) cc_final: 0.7525 (m-40) REVERT: H 59 MET cc_start: 0.9496 (mmm) cc_final: 0.9074 (mmm) REVERT: H 99 LEU cc_start: 0.9357 (mm) cc_final: 0.9152 (mp) REVERT: H 100 PRO cc_start: 0.8206 (Cg_exo) cc_final: 0.7323 (Cg_endo) REVERT: H 103 LEU cc_start: 0.8716 (mt) cc_final: 0.8336 (pp) REVERT: H 106 HIS cc_start: 0.9674 (m90) cc_final: 0.9329 (m-70) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1342 time to fit residues: 25.8532 Evaluate side-chains 94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 91 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 40.0000 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.045418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.038777 restraints weight = 146913.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.040110 restraints weight = 92350.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.041050 restraints weight = 63437.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.041728 restraints weight = 46277.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.042220 restraints weight = 35564.960| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12724 Z= 0.198 Angle : 0.757 13.482 18454 Z= 0.432 Chirality : 0.049 0.405 2110 Planarity : 0.006 0.061 1313 Dihedral : 32.591 179.807 4038 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.57 (0.29), residues: 728 helix: 1.17 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.54 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 29 TYR 0.026 0.002 TYR D 39 PHE 0.028 0.003 PHE A 104 HIS 0.013 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.20 (12724) covalent geometry : angle 0.75728 / 0.43 (18454) hydrogen bonds : bond 0.08875 / 5.90 ( 774) hydrogen bonds : angle 4.01213 / 2.92 ( 1921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.321 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: 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 97 GLU cc_start: 0.9122 (pt0) cc_final: 0.8702 (pt0) REVERT: A 100 LEU cc_start: 0.9804 (mt) cc_final: 0.9501 (mt) REVERT: A 120 MET cc_start: 0.9412 (mtt) cc_final: 0.9142 (mtt) REVERT: B 68 ASP cc_start: 0.9595 (m-30) cc_final: 0.9312 (m-30) REVERT: B 84 MET cc_start: 0.9188 (mmt) cc_final: 0.8833 (mpp) REVERT: B 98 TYR cc_start: 0.8493 (m-10) cc_final: 0.8185 (m-80) REVERT: C 64 GLU cc_start: 0.9455 (tt0) cc_final: 0.9174 (tp30) REVERT: C 68 ASN cc_start: 0.9297 (m-40) cc_final: 0.9054 (m110) REVERT: D 54 LYS cc_start: 0.9545 (mttt) cc_final: 0.9157 (tptp) REVERT: D 56 MET cc_start: 0.5225 (tpt) cc_final: 0.4610 (tpt) REVERT: D 59 MET cc_start: 0.9031 (mmp) cc_final: 0.8430 (tmm) REVERT: E 81 ASP cc_start: 0.6909 (t0) cc_final: 0.6065 (m-30) REVERT: E 92 LEU cc_start: 0.8652 (mt) cc_final: 0.8418 (mt) REVERT: E 94 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8894 (mm-30) REVERT: E 110 CYS cc_start: 0.8686 (m) cc_final: 0.8366 (m) REVERT: F 58 LEU cc_start: 0.9499 (tp) cc_final: 0.9018 (pp) REVERT: F 62 LEU cc_start: 0.9706 (mt) cc_final: 0.9373 (pp) REVERT: F 72 TYR cc_start: 0.9276 (m-80) cc_final: 0.8788 (m-80) REVERT: F 84 MET cc_start: 0.8598 (mmm) cc_final: 0.7784 (ttp) REVERT: G 94 ASN cc_start: 0.8060 (t0) cc_final: 0.7719 (m-40) REVERT: H 59 MET cc_start: 0.9409 (mmm) cc_final: 0.8969 (mmm) REVERT: H 103 LEU cc_start: 0.8776 (mt) cc_final: 0.8487 (mt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1206 time to fit residues: 21.7196 Evaluate side-chains 91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 97 optimal weight: 40.0000 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 overall best weight: 5.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.044876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038345 restraints weight = 147924.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.039674 restraints weight = 92249.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.040625 restraints weight = 63000.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.041304 restraints weight = 45758.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.041801 restraints weight = 34891.156| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12724 Z= 0.199 Angle : 0.763 13.699 18454 Z= 0.434 Chirality : 0.050 0.407 2110 Planarity : 0.006 0.061 1313 Dihedral : 32.708 179.910 4038 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.42 (0.29), residues: 728 helix: 1.06 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 96 TYR 0.030 0.002 TYR H 37 PHE 0.049 0.003 PHE G 25 HIS 0.008 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.20 (12724) covalent geometry : angle 0.76274 / 0.43 (18454) hydrogen bonds : bond 0.08921 / 5.93 ( 774) hydrogen bonds : angle 4.10536 / 3.01 ( 1921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.302 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9141 (pt0) cc_final: 0.8715 (pt0) REVERT: A 100 LEU cc_start: 0.9810 (mt) cc_final: 0.9494 (mt) REVERT: A 120 MET cc_start: 0.9403 (mtt) cc_final: 0.9039 (mtp) REVERT: B 84 MET cc_start: 0.9193 (mmt) cc_final: 0.8837 (mpp) REVERT: B 98 TYR cc_start: 0.8615 (m-10) cc_final: 0.8278 (m-80) REVERT: C 64 GLU cc_start: 0.9499 (tt0) cc_final: 0.9208 (tp30) REVERT: C 68 ASN cc_start: 0.9301 (m-40) cc_final: 0.8967 (m110) REVERT: D 54 LYS cc_start: 0.9556 (mttt) cc_final: 0.9205 (tptm) REVERT: E 81 ASP cc_start: 0.7003 (t0) cc_final: 0.6133 (m-30) REVERT: E 92 LEU cc_start: 0.8753 (mt) cc_final: 0.8451 (mt) REVERT: E 94 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8901 (mm-30) REVERT: F 25 ASN cc_start: 0.6509 (m-40) cc_final: 0.6077 (m110) REVERT: F 58 LEU cc_start: 0.9521 (tp) cc_final: 0.9056 (pp) REVERT: F 62 LEU cc_start: 0.9718 (mt) cc_final: 0.9391 (pp) REVERT: F 72 TYR cc_start: 0.9316 (m-80) cc_final: 0.8847 (m-80) REVERT: F 84 MET cc_start: 0.8615 (mmm) cc_final: 0.7842 (ttp) REVERT: G 57 TYR cc_start: 0.8569 (t80) cc_final: 0.8267 (t80) REVERT: G 94 ASN cc_start: 0.8073 (t0) cc_final: 0.7734 (m-40) REVERT: H 59 MET cc_start: 0.9393 (mmm) cc_final: 0.8894 (mmm) REVERT: H 103 LEU cc_start: 0.8600 (mt) cc_final: 0.8111 (mt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1239 time to fit residues: 22.0440 Evaluate side-chains 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 70 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.049137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043062 restraints weight = 145641.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044437 restraints weight = 88889.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045455 restraints weight = 60151.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.046161 restraints weight = 42303.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.046704 restraints weight = 31325.944| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12724 Z= 0.165 Angle : 0.728 13.639 18454 Z= 0.416 Chirality : 0.049 0.397 2110 Planarity : 0.005 0.055 1313 Dihedral : 32.705 179.918 4038 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.73 (0.29), residues: 728 helix: 1.28 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.46 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 96 TYR 0.022 0.002 TYR H 37 PHE 0.024 0.002 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.17 (12724) covalent geometry : angle 0.72807 / 0.42 (18454) hydrogen bonds : bond 0.06788 / 4.51 ( 774) hydrogen bonds : angle 3.88041 / 2.84 ( 1921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.10 seconds wall clock time: 29 minutes 14.98 seconds (1754.98 seconds total)