Starting phenix.real_space_refine on Wed Aug 5 08:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gxa_51645/08_2026/9gxa_51645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gxa_51645/08_2026/9gxa_51645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gxa_51645/08_2026/9gxa_51645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gxa_51645/08_2026/9gxa_51645.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gxa_51645/08_2026/9gxa_51645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gxa_51645/08_2026/9gxa_51645.map" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 224 5.49 5 S 8 5.16 5 C 5167 2.51 5 N 1696 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9215 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 575 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 516 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "C" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 628 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "E" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 628 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 565 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "G" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "H" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 541 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "I" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2292 Classifications: {'DNA': 112} Link IDs: {'rna3p': 111} Chain: "J" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2300 Classifications: {'DNA': 112} Link IDs: {'rna3p': 111} Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 9215 At special positions: 0 Unit cell: (86.92, 113.16, 121.36, 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 8 16.00 P 224 15.00 O 2120 8.00 N 1696 7.00 C 5167 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: 0.97 Conformation dependent library (CDL) restraints added in 183.2 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 78.7% alpha, 0.7% beta 108 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 66 through 80 removed outlier: 4.386A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 117 Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.191A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 90 removed outlier: 3.520A pdb=" N VAL B 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 90 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 116 removed outlier: 3.548A pdb=" N LEU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.649A pdb=" N VAL C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 4.272A pdb=" N GLU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.581A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.726A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.622A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.585A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.708A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 63 through 77 removed outlier: 3.733A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 117 Processing helix chain 'G' and resid 122 through 134 removed outlier: 3.729A pdb=" N VAL G 126 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.807A pdb=" N GLY H 28 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 removed outlier: 3.578A pdb=" N ILE H 34 " --> pdb=" O THR H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 76 removed outlier: 4.219A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA H 76 " --> pdb=" O TYR H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.519A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS H 91 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.361A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 120 through 121 323 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 258 hydrogen bonds 516 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1867 1.33 - 1.45: 3149 1.45 - 1.57: 4370 1.57 - 1.69: 446 1.69 - 1.81: 12 Bond restraints: 9844 Sorted by residual: bond pdb=" C3' DA I 20 " pdb=" C2' DA I 20 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DC I -4 " pdb=" C2' DC I -4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DA J -5 " pdb=" C2' DA J -5 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC I -20 " pdb=" C2' DC I -20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 bond pdb=" N THR C 120 " pdb=" CA THR C 120 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.31e-02 5.83e+03 9.75e+00 ... (remaining 9839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 12898 1.39 - 2.77: 1252 2.77 - 4.16: 97 4.16 - 5.55: 15 5.55 - 6.93: 3 Bond angle restraints: 14265 Sorted by residual: angle pdb=" N3 DT I 39 " pdb=" C4 DT I 39 " pdb=" O4 DT I 39 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 28 " pdb=" C4 DT I 28 " pdb=" O4 DT I 28 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I -3 " pdb=" C4 DT I -3 " pdb=" O4 DT I -3 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 14260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 4220 35.61 - 71.23: 1110 71.23 - 106.84: 21 106.84 - 142.46: 2 142.46 - 178.07: 2 Dihedral angle restraints: 5355 sinusoidal: 3693 harmonic: 1662 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DA J 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.07 -178.07 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 57 " pdb=" C3' DA I 57 " pdb=" O3' DA I 57 " pdb=" P DT I 58 " ideal model delta sinusoidal sigma weight residual 220.00 44.59 175.41 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 44 " pdb=" C3' DT J 44 " pdb=" O3' DT J 44 " pdb=" P DT J 45 " ideal model delta sinusoidal sigma weight residual -140.00 -0.19 -139.81 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 5352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1154 0.041 - 0.083: 334 0.083 - 0.124: 135 0.124 - 0.165: 10 0.165 - 0.207: 3 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CB VAL C 119 " pdb=" CA VAL C 119 " pdb=" CG1 VAL C 119 " pdb=" CG2 VAL C 119 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL E 82 " pdb=" CA VAL E 82 " pdb=" CG1 VAL E 82 " pdb=" CG2 VAL E 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA LYS H 31 " pdb=" N LYS H 31 " pdb=" C LYS H 31 " pdb=" CB LYS H 31 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1633 not shown) Planarity restraints: 1016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 5 " -0.005 2.00e-02 2.50e+03 1.18e-02 3.11e+00 pdb=" N1 DC J 5 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DC J 5 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC J 5 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DC J 5 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC J 5 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC J 5 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC J 5 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 5 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " -0.021 2.00e-02 2.50e+03 9.48e-03 2.47e+00 pdb=" N9 DA I 17 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -4 " 0.017 2.00e-02 2.50e+03 9.91e-03 2.21e+00 pdb=" N1 DC I -4 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DC I -4 " 0.012 2.00e-02 2.50e+03 pdb=" O2 DC I -4 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC I -4 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC I -4 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I -4 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC I -4 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC I -4 " -0.007 2.00e-02 2.50e+03 ... (remaining 1013 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 28 2.52 - 3.12: 6589 3.12 - 3.71: 17762 3.71 - 4.31: 22316 4.31 - 4.90: 31856 Nonbonded interactions: 78551 Sorted by model distance: nonbonded pdb=" CD1 LEU A 112 " pdb=" OD1 ASP A 125 " model vdw 1.931 3.460 nonbonded pdb=" CG2 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.121 3.460 nonbonded pdb=" OG1 THR F 30 " pdb=" OP1 DT I 18 " model vdw 2.126 3.040 nonbonded pdb=" NH2 ARG H 36 " pdb=" OP2 DG J -44 " model vdw 2.173 3.120 nonbonded pdb=" OD2 ASP C 108 " pdb=" NH1 ARG C 133 " model vdw 2.250 3.120 ... (remaining 78546 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 65 through 134) selection = (chain 'C' and resid 65 through 134) selection = (chain 'E' and resid 65 through 134) selection = (chain 'G' and resid 65 through 134) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 26 through 90) selection = (chain 'F' and resid 26 through 90) selection = (chain 'H' and resid 26 through 90) } 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: 3.290 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9844 Z= 0.529 Angle : 0.815 6.932 14265 Z= 0.724 Chirality : 0.045 0.207 1636 Planarity : 0.003 0.024 1016 Dihedral : 29.322 178.070 4275 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.35), residues: 558 helix: 1.74 (0.25), residues: 429 sheet: None (None), residues: 0 loop : -1.55 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 67 TYR 0.017 0.001 TYR E 110 PHE 0.022 0.001 PHE C 78 TRP 0.006 0.001 TRP E 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.53 ( 9844) covalent geometry : angle 0.81453 / 0.72 (14265) hydrogen bonds : bond 0.10209 / 6.68 ( 581) hydrogen bonds : angle 4.17625 / 3.09 ( 1470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.242 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: A 67 PHE cc_start: 0.7457 (t80) cc_final: 0.7201 (t80) REVERT: A 99 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6588 (mp0) REVERT: A 110 TYR cc_start: 0.8249 (t80) cc_final: 0.7894 (t80) REVERT: B 44 LYS cc_start: 0.8753 (mmpt) cc_final: 0.8546 (mmmt) REVERT: B 50 ILE cc_start: 0.8803 (tt) cc_final: 0.8482 (mt) REVERT: B 59 LYS cc_start: 0.9417 (tmtt) cc_final: 0.8951 (tmtt) REVERT: C 96 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6730 (tm-30) REVERT: H 49 LEU cc_start: 0.8650 (tp) cc_final: 0.8153 (tp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1275 time to fit residues: 28.3057 Evaluate side-chains 122 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.045711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.034548 restraints weight = 82904.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.035473 restraints weight = 45921.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.036047 restraints weight = 31786.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036449 restraints weight = 25364.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036678 restraints weight = 21884.956| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9844 Z= 0.211 Angle : 0.759 9.338 14265 Z= 0.436 Chirality : 0.048 0.254 1636 Planarity : 0.005 0.044 1016 Dihedral : 32.625 178.109 3157 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.34), residues: 558 helix: 1.63 (0.24), residues: 427 sheet: None (None), residues: 0 loop : -1.81 (0.44), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.036 0.002 TYR D 88 PHE 0.027 0.002 PHE C 78 TRP 0.008 0.002 TRP E 86 HIS 0.007 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.21 ( 9844) covalent geometry : angle 0.75857 / 0.44 (14265) hydrogen bonds : bond 0.06681 / 4.49 ( 581) hydrogen bonds : angle 3.57610 / 2.65 ( 1470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 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: A 99 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6954 (mp0) REVERT: A 110 TYR cc_start: 0.9152 (t80) cc_final: 0.8860 (t80) REVERT: A 131 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8686 (ttp80) REVERT: B 44 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8665 (mmmt) REVERT: B 59 LYS cc_start: 0.9715 (tmtt) cc_final: 0.9170 (tptt) REVERT: B 85 ASP cc_start: 0.7443 (m-30) cc_final: 0.7003 (m-30) REVERT: C 73 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8661 (tm-30) REVERT: C 107 GLU cc_start: 0.8648 (pt0) cc_final: 0.8313 (pt0) REVERT: D 74 GLU cc_start: 0.9226 (tp30) cc_final: 0.9007 (tm-30) REVERT: E 73 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8632 (tm-30) REVERT: E 89 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8216 (tp-100) REVERT: E 99 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8410 (tm-30) REVERT: F 63 GLU cc_start: 0.8812 (tp30) cc_final: 0.8483 (tp30) REVERT: F 67 ARG cc_start: 0.9205 (mtp-110) cc_final: 0.8926 (mtp-110) REVERT: G 96 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8610 (tm-30) REVERT: G 101 PHE cc_start: 0.9409 (t80) cc_final: 0.8896 (t80) REVERT: G 107 GLU cc_start: 0.9251 (pt0) cc_final: 0.8936 (pp20) REVERT: H 53 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9219 (tt0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1199 time to fit residues: 24.2181 Evaluate side-chains 117 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 40.0000 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.044972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.033986 restraints weight = 82376.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.034900 restraints weight = 44921.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035527 restraints weight = 30848.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.035926 restraints weight = 24166.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036145 restraints weight = 20863.088| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9844 Z= 0.192 Angle : 0.730 10.142 14265 Z= 0.421 Chirality : 0.047 0.257 1636 Planarity : 0.005 0.042 1016 Dihedral : 32.832 178.722 3157 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.34), residues: 558 helix: 1.52 (0.24), residues: 426 sheet: None (None), residues: 0 loop : -1.86 (0.43), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 118 TYR 0.029 0.002 TYR E 110 PHE 0.028 0.002 PHE G 67 TRP 0.015 0.002 TRP G 86 HIS 0.006 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.19 ( 9844) covalent geometry : angle 0.73002 / 0.42 (14265) hydrogen bonds : bond 0.06212 / 4.16 ( 581) hydrogen bonds : angle 3.44213 / 2.54 ( 1470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6987 (mp0) REVERT: A 107 GLU cc_start: 0.9147 (pt0) cc_final: 0.8763 (pt0) REVERT: A 110 TYR cc_start: 0.9140 (t80) cc_final: 0.8868 (t80) REVERT: A 131 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8732 (ttp80) REVERT: B 44 LYS cc_start: 0.9122 (mmpt) cc_final: 0.8723 (mmmt) REVERT: B 59 LYS cc_start: 0.9712 (tmtt) cc_final: 0.9167 (tptt) REVERT: B 85 ASP cc_start: 0.7631 (m-30) cc_final: 0.6984 (m-30) REVERT: C 73 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8639 (tm-30) REVERT: D 63 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8317 (tm-30) REVERT: D 92 ARG cc_start: 0.8806 (tpt90) cc_final: 0.8599 (tpt90) REVERT: E 89 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8185 (tp-100) REVERT: E 96 GLU cc_start: 0.8902 (tp30) cc_final: 0.8646 (tp30) REVERT: E 107 GLU cc_start: 0.8431 (pt0) cc_final: 0.8138 (pp20) REVERT: F 82 THR cc_start: 0.9068 (m) cc_final: 0.8728 (p) REVERT: G 101 PHE cc_start: 0.9412 (t80) cc_final: 0.8870 (t80) REVERT: G 131 ARG cc_start: 0.9387 (ptm-80) cc_final: 0.9044 (ptm-80) REVERT: H 67 ARG cc_start: 0.9584 (tpp80) cc_final: 0.9232 (mmt180) REVERT: H 68 ASP cc_start: 0.9190 (m-30) cc_final: 0.8779 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0963 time to fit residues: 19.4445 Evaluate side-chains 116 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.044331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.033373 restraints weight = 83353.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034287 restraints weight = 45635.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.034928 restraints weight = 31474.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035333 restraints weight = 24555.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035596 restraints weight = 21069.355| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9844 Z= 0.201 Angle : 0.747 9.923 14265 Z= 0.425 Chirality : 0.047 0.259 1636 Planarity : 0.005 0.040 1016 Dihedral : 32.929 179.378 3157 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.34), residues: 558 helix: 1.59 (0.24), residues: 419 sheet: None (None), residues: 0 loop : -1.89 (0.43), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 80 TYR 0.020 0.002 TYR E 110 PHE 0.027 0.002 PHE C 78 TRP 0.004 0.001 TRP C 86 HIS 0.006 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.20 ( 9844) covalent geometry : angle 0.74700 / 0.43 (14265) hydrogen bonds : bond 0.06588 / 4.40 ( 581) hydrogen bonds : angle 3.49057 / 2.56 ( 1470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7087 (mp0) REVERT: A 110 TYR cc_start: 0.9133 (t80) cc_final: 0.8814 (t80) REVERT: A 131 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8803 (ttp80) REVERT: B 44 LYS cc_start: 0.9097 (mmpt) cc_final: 0.8674 (mmmt) REVERT: B 59 LYS cc_start: 0.9709 (tmtt) cc_final: 0.9398 (tptt) REVERT: B 84 MET cc_start: 0.6775 (mmp) cc_final: 0.6131 (mmp) REVERT: B 85 ASP cc_start: 0.7592 (m-30) cc_final: 0.7016 (m-30) REVERT: C 73 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8651 (tm-30) REVERT: C 96 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 107 GLU cc_start: 0.8912 (pt0) cc_final: 0.8638 (pp20) REVERT: D 44 LYS cc_start: 0.9496 (mmtm) cc_final: 0.9238 (mmtm) REVERT: D 63 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8268 (tm-30) REVERT: D 68 ASP cc_start: 0.8805 (m-30) cc_final: 0.8603 (m-30) REVERT: E 89 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8186 (tp-100) REVERT: E 130 ARG cc_start: 0.8813 (tpt-90) cc_final: 0.8597 (tpp80) REVERT: F 82 THR cc_start: 0.9084 (m) cc_final: 0.8815 (p) REVERT: G 101 PHE cc_start: 0.9406 (t80) cc_final: 0.8880 (t80) REVERT: G 131 ARG cc_start: 0.9414 (ptm-80) cc_final: 0.9173 (ptm-80) REVERT: H 31 LYS cc_start: 0.9626 (ptpp) cc_final: 0.9371 (pttm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1101 time to fit residues: 20.8103 Evaluate side-chains 113 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.045418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.034360 restraints weight = 82976.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.035294 restraints weight = 45428.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.035909 restraints weight = 31174.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.036323 restraints weight = 24610.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036565 restraints weight = 21257.150| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9844 Z= 0.142 Angle : 0.704 10.232 14265 Z= 0.403 Chirality : 0.046 0.263 1636 Planarity : 0.004 0.051 1016 Dihedral : 32.901 179.494 3157 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.34), residues: 558 helix: 1.64 (0.24), residues: 426 sheet: None (None), residues: 0 loop : -1.67 (0.44), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 69 TYR 0.023 0.002 TYR E 110 PHE 0.020 0.001 PHE D 61 TRP 0.006 0.001 TRP A 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 ( 9844) covalent geometry : angle 0.70418 / 0.40 (14265) hydrogen bonds : bond 0.04727 / 3.16 ( 581) hydrogen bonds : angle 3.27076 / 2.40 ( 1470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7149 (mp0) REVERT: A 107 GLU cc_start: 0.9105 (pt0) cc_final: 0.8713 (pt0) REVERT: A 110 TYR cc_start: 0.9101 (t80) cc_final: 0.8803 (t80) REVERT: A 131 ARG cc_start: 0.9096 (ttp80) cc_final: 0.8793 (ttp80) REVERT: B 44 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8631 (mmmt) REVERT: B 59 LYS cc_start: 0.9708 (tmtt) cc_final: 0.9393 (tptt) REVERT: B 84 MET cc_start: 0.6791 (mmp) cc_final: 0.6075 (mmp) REVERT: B 85 ASP cc_start: 0.7588 (m-30) cc_final: 0.6938 (m-30) REVERT: C 73 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8665 (tm-30) REVERT: C 96 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7369 (tm-30) REVERT: C 107 GLU cc_start: 0.8890 (pt0) cc_final: 0.8593 (pp20) REVERT: D 44 LYS cc_start: 0.9490 (mmtm) cc_final: 0.9243 (mmtm) REVERT: D 63 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8153 (tm-30) REVERT: D 92 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8510 (tpt170) REVERT: E 89 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8126 (tp-100) REVERT: F 50 ILE cc_start: 0.9502 (tp) cc_final: 0.9168 (tp) REVERT: F 82 THR cc_start: 0.9015 (m) cc_final: 0.8662 (p) REVERT: F 92 ARG cc_start: 0.8557 (tpt-90) cc_final: 0.8161 (tpt-90) REVERT: G 72 ARG cc_start: 0.9079 (mtt-85) cc_final: 0.8661 (tpp-160) REVERT: G 101 PHE cc_start: 0.9374 (t80) cc_final: 0.8851 (t80) REVERT: G 107 GLU cc_start: 0.9230 (pt0) cc_final: 0.8809 (pp20) REVERT: G 131 ARG cc_start: 0.9384 (ptm-80) cc_final: 0.8856 (ttp80) REVERT: H 31 LYS cc_start: 0.9617 (ptpp) cc_final: 0.9361 (pttm) REVERT: H 49 LEU cc_start: 0.9235 (tp) cc_final: 0.8803 (tp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1173 time to fit residues: 22.5040 Evaluate side-chains 116 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.045372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.034386 restraints weight = 84247.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035325 restraints weight = 46112.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035941 restraints weight = 31647.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036345 restraints weight = 24887.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036614 restraints weight = 21428.730| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9844 Z= 0.148 Angle : 0.707 10.333 14265 Z= 0.404 Chirality : 0.045 0.265 1636 Planarity : 0.004 0.057 1016 Dihedral : 32.835 179.817 3157 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.21 % Allowed : 2.10 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.34), residues: 558 helix: 1.67 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.53 (0.45), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.021 0.002 TYR E 110 PHE 0.032 0.002 PHE G 67 TRP 0.005 0.001 TRP E 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 ( 9844) covalent geometry : angle 0.70662 / 0.40 (14265) hydrogen bonds : bond 0.04843 / 3.22 ( 581) hydrogen bonds : angle 3.25225 / 2.39 ( 1470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8150 (pmt-80) cc_final: 0.7672 (pmt-80) REVERT: A 99 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7331 (mp0) REVERT: A 107 GLU cc_start: 0.9085 (pt0) cc_final: 0.8670 (pt0) REVERT: A 110 TYR cc_start: 0.9115 (t80) cc_final: 0.8829 (t80) REVERT: A 131 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8841 (ttp80) REVERT: B 44 LYS cc_start: 0.9046 (mmpt) cc_final: 0.8638 (mmmt) REVERT: B 59 LYS cc_start: 0.9707 (tmtt) cc_final: 0.9399 (tptt) REVERT: B 84 MET cc_start: 0.6769 (mmp) cc_final: 0.6107 (mmp) REVERT: B 85 ASP cc_start: 0.7525 (m-30) cc_final: 0.6917 (m-30) REVERT: C 73 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 96 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 107 GLU cc_start: 0.8918 (pt0) cc_final: 0.8617 (pp20) REVERT: D 44 LYS cc_start: 0.9494 (mmtm) cc_final: 0.9226 (mmtm) REVERT: D 53 GLU cc_start: 0.8965 (tp30) cc_final: 0.8664 (tp30) REVERT: D 63 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 67 ARG cc_start: 0.8949 (ttp-170) cc_final: 0.8650 (ttp80) REVERT: D 92 ARG cc_start: 0.8709 (tpt90) cc_final: 0.8454 (tpt90) REVERT: E 89 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8099 (tp-100) REVERT: E 96 GLU cc_start: 0.9036 (tp30) cc_final: 0.8777 (tp30) REVERT: F 50 ILE cc_start: 0.9387 (tp) cc_final: 0.8959 (tp) REVERT: F 82 THR cc_start: 0.9017 (m) cc_final: 0.8692 (p) REVERT: G 72 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8503 (tpp-160) REVERT: G 101 PHE cc_start: 0.9379 (t80) cc_final: 0.8879 (t80) REVERT: G 107 GLU cc_start: 0.9226 (pt0) cc_final: 0.8808 (pp20) REVERT: G 108 ASP cc_start: 0.8631 (m-30) cc_final: 0.7428 (m-30) REVERT: G 131 ARG cc_start: 0.9359 (ptm-80) cc_final: 0.9116 (ptm-80) REVERT: H 31 LYS cc_start: 0.9627 (ptpp) cc_final: 0.9380 (pttm) REVERT: H 49 LEU cc_start: 0.9203 (tp) cc_final: 0.8677 (tp) REVERT: H 67 ARG cc_start: 0.9576 (tpp80) cc_final: 0.9224 (mmt-90) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.1137 time to fit residues: 22.5970 Evaluate side-chains 122 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.045678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.034792 restraints weight = 83549.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035742 restraints weight = 45684.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.036357 restraints weight = 31312.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.036778 restraints weight = 24590.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.036949 restraints weight = 21077.177| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9844 Z= 0.143 Angle : 0.705 9.692 14265 Z= 0.402 Chirality : 0.045 0.267 1636 Planarity : 0.004 0.041 1016 Dihedral : 32.792 179.912 3157 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.34), residues: 558 helix: 1.72 (0.24), residues: 427 sheet: None (None), residues: 0 loop : -1.41 (0.46), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.024 0.002 TYR E 110 PHE 0.019 0.001 PHE D 61 TRP 0.005 0.001 TRP C 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 ( 9844) covalent geometry : angle 0.70507 / 0.40 (14265) hydrogen bonds : bond 0.04537 / 3.02 ( 581) hydrogen bonds : angle 3.24897 / 2.39 ( 1470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7315 (mp0) REVERT: A 107 GLU cc_start: 0.9080 (pt0) cc_final: 0.8674 (pt0) REVERT: A 110 TYR cc_start: 0.9086 (t80) cc_final: 0.8824 (t80) REVERT: A 131 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8871 (ttp80) REVERT: B 44 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8634 (mmmt) REVERT: B 50 ILE cc_start: 0.9559 (tt) cc_final: 0.9181 (tt) REVERT: B 59 LYS cc_start: 0.9708 (tmtt) cc_final: 0.9390 (tptt) REVERT: B 84 MET cc_start: 0.6817 (mmp) cc_final: 0.6103 (mmp) REVERT: B 85 ASP cc_start: 0.7550 (m-30) cc_final: 0.6856 (m-30) REVERT: C 73 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8589 (tm-30) REVERT: C 96 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 107 GLU cc_start: 0.8901 (pt0) cc_final: 0.8602 (pp20) REVERT: D 44 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9229 (mmtm) REVERT: D 49 LEU cc_start: 0.9515 (mp) cc_final: 0.9315 (mp) REVERT: D 53 GLU cc_start: 0.8929 (tp30) cc_final: 0.8654 (tp30) REVERT: D 63 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8077 (tm-30) REVERT: D 67 ARG cc_start: 0.8957 (ttp-170) cc_final: 0.8660 (ttp80) REVERT: D 68 ASP cc_start: 0.8703 (m-30) cc_final: 0.8402 (m-30) REVERT: D 92 ARG cc_start: 0.8712 (tpt90) cc_final: 0.8489 (tpt90) REVERT: E 89 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8069 (tp-100) REVERT: F 82 THR cc_start: 0.9030 (m) cc_final: 0.8714 (p) REVERT: F 92 ARG cc_start: 0.8654 (tpt-90) cc_final: 0.8006 (tpt-90) REVERT: G 72 ARG cc_start: 0.8907 (mtt-85) cc_final: 0.8376 (tpp-160) REVERT: G 101 PHE cc_start: 0.9381 (t80) cc_final: 0.8873 (t80) REVERT: G 107 GLU cc_start: 0.9214 (pt0) cc_final: 0.8813 (pp20) REVERT: G 108 ASP cc_start: 0.8666 (m-30) cc_final: 0.7335 (m-30) REVERT: G 110 TYR cc_start: 0.9325 (t80) cc_final: 0.8888 (t80) REVERT: G 131 ARG cc_start: 0.9357 (ptm-80) cc_final: 0.9111 (ptm-80) REVERT: H 31 LYS cc_start: 0.9624 (ptpp) cc_final: 0.9385 (pttm) REVERT: H 44 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8750 (mmmm) REVERT: H 49 LEU cc_start: 0.9195 (tp) cc_final: 0.8617 (tp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1081 time to fit residues: 21.0311 Evaluate side-chains 117 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.045925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035143 restraints weight = 81708.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036091 restraints weight = 44842.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.036705 restraints weight = 30739.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.037129 restraints weight = 24163.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.037355 restraints weight = 20700.666| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9844 Z= 0.142 Angle : 0.709 9.142 14265 Z= 0.405 Chirality : 0.045 0.268 1636 Planarity : 0.004 0.073 1016 Dihedral : 32.756 179.584 3157 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.34), residues: 558 helix: 1.71 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 69 TYR 0.028 0.002 TYR E 110 PHE 0.020 0.002 PHE D 61 TRP 0.005 0.001 TRP C 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 ( 9844) covalent geometry : angle 0.70871 / 0.41 (14265) hydrogen bonds : bond 0.04498 / 2.99 ( 581) hydrogen bonds : angle 3.26157 / 2.41 ( 1470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.221 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: A 69 ARG cc_start: 0.8054 (pmt-80) cc_final: 0.7432 (pmt-80) REVERT: A 99 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7354 (mp0) REVERT: A 107 GLU cc_start: 0.9092 (pt0) cc_final: 0.8675 (pt0) REVERT: A 110 TYR cc_start: 0.9100 (t80) cc_final: 0.8848 (t80) REVERT: B 44 LYS cc_start: 0.9032 (mmpt) cc_final: 0.8593 (mmmt) REVERT: B 59 LYS cc_start: 0.9713 (tmtt) cc_final: 0.9401 (tptt) REVERT: B 84 MET cc_start: 0.6710 (mmp) cc_final: 0.6015 (mmp) REVERT: B 85 ASP cc_start: 0.7447 (m-30) cc_final: 0.6854 (m-30) REVERT: C 73 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 96 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7400 (tm-30) REVERT: C 107 GLU cc_start: 0.8905 (pt0) cc_final: 0.8596 (pp20) REVERT: D 44 LYS cc_start: 0.9478 (mmtm) cc_final: 0.9237 (mmtm) REVERT: D 53 GLU cc_start: 0.8940 (tp30) cc_final: 0.8601 (tp30) REVERT: D 63 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 67 ARG cc_start: 0.8958 (ttp-170) cc_final: 0.8604 (ttp80) REVERT: D 68 ASP cc_start: 0.8696 (m-30) cc_final: 0.8403 (m-30) REVERT: D 92 ARG cc_start: 0.8714 (tpt90) cc_final: 0.8496 (tpt90) REVERT: E 89 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8052 (tp-100) REVERT: F 82 THR cc_start: 0.9021 (m) cc_final: 0.8699 (p) REVERT: F 92 ARG cc_start: 0.8618 (tpt-90) cc_final: 0.7926 (tpt-90) REVERT: G 101 PHE cc_start: 0.9375 (t80) cc_final: 0.8884 (t80) REVERT: G 107 GLU cc_start: 0.9187 (pt0) cc_final: 0.8805 (pp20) REVERT: G 108 ASP cc_start: 0.8698 (m-30) cc_final: 0.7431 (m-30) REVERT: G 110 TYR cc_start: 0.9338 (t80) cc_final: 0.8993 (t80) REVERT: H 31 LYS cc_start: 0.9607 (ptpp) cc_final: 0.9389 (pttm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1130 time to fit residues: 22.2142 Evaluate side-chains 119 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 20.0000 chunk 64 optimal weight: 40.0000 chunk 57 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.043675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.032989 restraints weight = 82715.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.033896 restraints weight = 45817.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034490 restraints weight = 31600.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.034865 restraints weight = 24933.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035123 restraints weight = 21409.757| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9844 Z= 0.220 Angle : 0.762 8.963 14265 Z= 0.431 Chirality : 0.046 0.268 1636 Planarity : 0.005 0.061 1016 Dihedral : 32.943 178.645 3157 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.34), residues: 558 helix: 1.75 (0.24), residues: 420 sheet: None (None), residues: 0 loop : -1.42 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 131 TYR 0.022 0.002 TYR E 110 PHE 0.024 0.002 PHE C 78 TRP 0.004 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.22 ( 9844) covalent geometry : angle 0.76241 / 0.43 (14265) hydrogen bonds : bond 0.07434 / 4.98 ( 581) hydrogen bonds : angle 3.52302 / 2.61 ( 1470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 107 GLU cc_start: 0.9106 (pt0) cc_final: 0.8703 (pt0) REVERT: A 110 TYR cc_start: 0.9102 (t80) cc_final: 0.8846 (t80) REVERT: B 44 LYS cc_start: 0.9060 (mmpt) cc_final: 0.8591 (mmmt) REVERT: B 84 MET cc_start: 0.6899 (mmp) cc_final: 0.6249 (mmp) REVERT: B 85 ASP cc_start: 0.7601 (m-30) cc_final: 0.6965 (m-30) REVERT: C 73 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 107 GLU cc_start: 0.8888 (pt0) cc_final: 0.8579 (pp20) REVERT: D 44 LYS cc_start: 0.9504 (mmtm) cc_final: 0.9228 (mmtm) REVERT: D 53 GLU cc_start: 0.9020 (tp30) cc_final: 0.8714 (tp30) REVERT: D 63 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 67 ARG cc_start: 0.8972 (ttp-170) cc_final: 0.8653 (ttp80) REVERT: D 68 ASP cc_start: 0.8789 (m-30) cc_final: 0.8530 (m-30) REVERT: E 89 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8106 (tp-100) REVERT: F 82 THR cc_start: 0.9032 (m) cc_final: 0.8797 (p) REVERT: G 101 PHE cc_start: 0.9401 (t80) cc_final: 0.8955 (t80) REVERT: G 107 GLU cc_start: 0.9247 (pt0) cc_final: 0.8835 (pp20) REVERT: G 108 ASP cc_start: 0.8864 (m-30) cc_final: 0.7472 (m-30) REVERT: G 110 TYR cc_start: 0.9355 (t80) cc_final: 0.9086 (t80) REVERT: H 31 LYS cc_start: 0.9632 (ptpp) cc_final: 0.9426 (pttm) REVERT: H 49 LEU cc_start: 0.9216 (tp) cc_final: 0.8645 (tp) REVERT: H 67 ARG cc_start: 0.9577 (tpp80) cc_final: 0.9217 (mmt180) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1120 time to fit residues: 20.9281 Evaluate side-chains 111 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 20.0000 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.044895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.034124 restraints weight = 81925.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035071 restraints weight = 45400.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035683 restraints weight = 31207.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036072 restraints weight = 24550.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036357 restraints weight = 21121.881| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9844 Z= 0.150 Angle : 0.738 9.278 14265 Z= 0.416 Chirality : 0.046 0.266 1636 Planarity : 0.004 0.035 1016 Dihedral : 32.981 179.055 3157 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.34), residues: 558 helix: 1.68 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.49 (0.44), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 131 TYR 0.022 0.002 TYR E 110 PHE 0.023 0.002 PHE D 61 TRP 0.005 0.001 TRP A 86 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 ( 9844) covalent geometry : angle 0.73849 / 0.42 (14265) hydrogen bonds : bond 0.04610 / 3.07 ( 581) hydrogen bonds : angle 3.34444 / 2.49 ( 1470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.254 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: A 99 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7357 (mp0) REVERT: A 107 GLU cc_start: 0.9099 (pt0) cc_final: 0.8681 (pt0) REVERT: A 110 TYR cc_start: 0.9082 (t80) cc_final: 0.8824 (t80) REVERT: B 44 LYS cc_start: 0.9066 (mmpt) cc_final: 0.8659 (mmmt) REVERT: B 84 MET cc_start: 0.6954 (mmp) cc_final: 0.6694 (mmp) REVERT: B 85 ASP cc_start: 0.7460 (m-30) cc_final: 0.6880 (m-30) REVERT: C 73 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8663 (tm-30) REVERT: C 96 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7330 (tm-30) REVERT: C 107 GLU cc_start: 0.8897 (pt0) cc_final: 0.8569 (pp20) REVERT: D 44 LYS cc_start: 0.9497 (mmtm) cc_final: 0.9274 (mmtm) REVERT: D 53 GLU cc_start: 0.8959 (tp30) cc_final: 0.8666 (tp30) REVERT: D 63 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8115 (tm-30) REVERT: D 67 ARG cc_start: 0.8963 (ttp-170) cc_final: 0.8641 (ttp80) REVERT: E 89 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8072 (tp-100) REVERT: E 96 GLU cc_start: 0.8155 (tp30) cc_final: 0.7172 (tp30) REVERT: E 99 GLU cc_start: 0.7930 (pp20) cc_final: 0.7509 (pp20) REVERT: F 82 THR cc_start: 0.9015 (m) cc_final: 0.8708 (p) REVERT: F 92 ARG cc_start: 0.8511 (tpt-90) cc_final: 0.8170 (tmm160) REVERT: G 101 PHE cc_start: 0.9366 (t80) cc_final: 0.8922 (t80) REVERT: G 107 GLU cc_start: 0.9181 (pt0) cc_final: 0.8820 (pp20) REVERT: G 108 ASP cc_start: 0.8720 (m-30) cc_final: 0.7416 (m-30) REVERT: G 110 TYR cc_start: 0.9357 (t80) cc_final: 0.9077 (t80) REVERT: H 49 LEU cc_start: 0.9188 (tp) cc_final: 0.8707 (tp) REVERT: H 67 ARG cc_start: 0.9563 (tpp80) cc_final: 0.9297 (mmt180) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1134 time to fit residues: 22.0057 Evaluate side-chains 116 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 30.0000 chunk 64 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.044337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.033622 restraints weight = 83736.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.034528 restraints weight = 46366.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.035118 restraints weight = 31956.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035520 restraints weight = 25195.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035742 restraints weight = 21646.959| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9844 Z= 0.167 Angle : 0.736 8.735 14265 Z= 0.416 Chirality : 0.045 0.269 1636 Planarity : 0.004 0.035 1016 Dihedral : 32.968 178.725 3157 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.34), residues: 558 helix: 1.82 (0.24), residues: 420 sheet: None (None), residues: 0 loop : -1.46 (0.44), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 131 TYR 0.021 0.002 TYR E 110 PHE 0.021 0.002 PHE D 61 TRP 0.003 0.001 TRP C 86 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 ( 9844) covalent geometry : angle 0.73617 / 0.42 (14265) hydrogen bonds : bond 0.05433 / 3.59 ( 581) hydrogen bonds : angle 3.37580 / 2.50 ( 1470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.92 seconds wall clock time: 25 minutes 7.18 seconds (1507.18 seconds total)