Starting phenix.real_space_refine on Thu Jul 2 15:04:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gxa_51645/07_2026/9gxa_51645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gxa_51645/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gxa_51645/07_2026/9gxa_51645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gxa_51645/07_2026/9gxa_51645.map" model { file = "/net/cci-nas-00/data/ceres_data/9gxa_51645/07_2026/9gxa_51645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gxa_51645/07_2026/9gxa_51645.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 1.66, per 1000 atoms: 0.18 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: 0.73 Conformation dependent library (CDL) restraints added in 253.8 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: 0.95 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: 1.60 Time building geometry restraints manager: 0.99 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: 12920 1.39 - 2.77: 1230 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: 3.840 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.300 ------------------------------------------------------------------------------- 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= 0.528 Angle : 0.808 6.932 14265 Z= 0.718 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 0.80823 / 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 : 0.226 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 67 PHE cc_start: 0.7457 (t80) cc_final: 0.7199 (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: 0.7896 (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: 0.8484 (mt) REVERT: B 59 LYS cc_start: 0.9417 (tmtt) cc_final: 0.8952 (tmtt) REVERT: C 96 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6725 (tm-30) REVERT: H 49 LEU cc_start: 0.8650 (tp) cc_final: 0.8151 (tp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1200 time to fit residues: 26.6327 Evaluate side-chains 118 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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: 20.0000 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: 2.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.045790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.034636 restraints weight = 82687.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.035573 restraints weight = 45601.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.036161 restraints weight = 31474.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036567 restraints weight = 24942.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036755 restraints weight = 21540.869| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9844 Z= 0.196 Angle : 0.740 10.858 14265 Z= 0.429 Chirality : 0.047 0.236 1636 Planarity : 0.005 0.041 1016 Dihedral : 32.752 178.155 3157 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.34), residues: 558 helix: 1.58 (0.24), residues: 427 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.036 0.002 TYR D 88 PHE 0.028 0.002 PHE C 78 TRP 0.009 0.002 TRP E 86 HIS 0.006 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 ( 9844) covalent geometry : angle 0.74044 / 0.43 (14265) hydrogen bonds : bond 0.06457 / 4.36 ( 581) hydrogen bonds : angle 3.49222 / 2.58 ( 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 159 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.263 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: 0.7501 (mt-10) cc_final: 0.6966 (mp0) REVERT: B 44 LYS cc_start: 0.9121 (mmpt) cc_final: 0.8788 (mmmt) REVERT: B 59 LYS cc_start: 0.9706 (tmtt) cc_final: 0.9149 (tptt) REVERT: B 85 ASP cc_start: 0.7424 (m-30) cc_final: 0.6981 (m-30) REVERT: C 73 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8645 (tm-30) REVERT: C 107 GLU cc_start: 0.8668 (pt0) cc_final: 0.8365 (pt0) REVERT: C 124 LYS cc_start: 0.9327 (pttp) cc_final: 0.8946 (pttp) REVERT: E 73 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8636 (tm-30) REVERT: E 87 GLN cc_start: 0.9403 (tt0) cc_final: 0.8627 (mt0) REVERT: E 89 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8184 (tp-100) REVERT: E 99 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8394 (tm-30) REVERT: F 63 GLU cc_start: 0.8813 (tp30) cc_final: 0.8484 (tp30) REVERT: F 67 ARG cc_start: 0.9204 (mtp-110) cc_final: 0.8927 (mtp-110) REVERT: G 96 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8610 (tm-30) REVERT: G 101 PHE cc_start: 0.9403 (t80) cc_final: 0.8883 (t80) REVERT: G 107 GLU cc_start: 0.9257 (pt0) cc_final: 0.8932 (pp20) REVERT: G 108 ASP cc_start: 0.8735 (m-30) cc_final: 0.7523 (m-30) REVERT: G 110 TYR cc_start: 0.9354 (t80) cc_final: 0.8878 (t80) REVERT: H 53 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9224 (tt0) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1138 time to fit residues: 23.3499 Evaluate side-chains 120 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 0.0370 chunk 51 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 40.0000 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.045071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.034161 restraints weight = 81720.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035077 restraints weight = 44665.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035694 restraints weight = 30683.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036065 restraints weight = 24127.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036315 restraints weight = 20894.890| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9844 Z= 0.200 Angle : 0.722 10.389 14265 Z= 0.419 Chirality : 0.046 0.234 1636 Planarity : 0.005 0.038 1016 Dihedral : 32.901 179.634 3157 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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: 1.03 (0.34), residues: 558 helix: 1.48 (0.24), residues: 426 sheet: None (None), residues: 0 loop : -2.02 (0.43), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 118 TYR 0.028 0.002 TYR E 110 PHE 0.028 0.002 PHE G 67 TRP 0.007 0.001 TRP E 86 HIS 0.006 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.20 ( 9844) covalent geometry : angle 0.72194 / 0.42 (14265) hydrogen bonds : bond 0.06430 / 4.32 ( 581) hydrogen bonds : angle 3.44940 / 2.55 ( 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 156 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 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: A 99 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6989 (mp0) REVERT: A 107 GLU cc_start: 0.9143 (pt0) cc_final: 0.8775 (pt0) REVERT: A 131 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8735 (ttp80) REVERT: B 44 LYS cc_start: 0.9162 (mmpt) cc_final: 0.8693 (mmmt) REVERT: B 59 LYS cc_start: 0.9708 (tmtt) cc_final: 0.9167 (tptt) REVERT: B 85 ASP cc_start: 0.7627 (m-30) cc_final: 0.6988 (m-30) REVERT: C 73 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 124 LYS cc_start: 0.9308 (pttp) cc_final: 0.8849 (pttm) REVERT: D 63 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8321 (tm-30) REVERT: E 87 GLN cc_start: 0.9408 (tt0) cc_final: 0.8650 (mt0) REVERT: E 89 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8176 (tp-100) REVERT: E 96 GLU cc_start: 0.8947 (tp30) cc_final: 0.8642 (tp30) REVERT: E 107 GLU cc_start: 0.8373 (pt0) cc_final: 0.8087 (pp20) REVERT: G 101 PHE cc_start: 0.9416 (t80) cc_final: 0.8871 (t80) REVERT: G 107 GLU cc_start: 0.9260 (pt0) cc_final: 0.8938 (pp20) REVERT: G 131 ARG cc_start: 0.9383 (ptm-80) cc_final: 0.9041 (ptm-80) REVERT: H 67 ARG cc_start: 0.9598 (tpp80) cc_final: 0.9258 (mmt180) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1032 time to fit residues: 21.2083 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 : 0.242 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.043898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.032940 restraints weight = 85097.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.033839 restraints weight = 46524.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.034453 restraints weight = 31995.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.034849 restraints weight = 25213.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.035071 restraints weight = 21740.238| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9844 Z= 0.223 Angle : 0.751 11.249 14265 Z= 0.430 Chirality : 0.047 0.239 1636 Planarity : 0.005 0.034 1016 Dihedral : 33.071 179.715 3157 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.34), residues: 558 helix: 1.57 (0.24), residues: 419 sheet: None (None), residues: 0 loop : -2.00 (0.44), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.023 0.002 TYR E 110 PHE 0.029 0.002 PHE C 78 TRP 0.005 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.22 ( 9844) covalent geometry : angle 0.75088 / 0.43 (14265) hydrogen bonds : bond 0.07229 / 4.86 ( 581) hydrogen bonds : angle 3.53566 / 2.59 ( 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 146 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7095 (mp0) REVERT: A 131 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8819 (ttp80) REVERT: B 44 LYS cc_start: 0.9145 (mmpt) cc_final: 0.8674 (mmmt) REVERT: B 59 LYS cc_start: 0.9713 (tmtt) cc_final: 0.9403 (tptt) REVERT: B 84 MET cc_start: 0.6768 (mmp) cc_final: 0.6126 (mmp) REVERT: B 85 ASP cc_start: 0.7602 (m-30) cc_final: 0.7047 (m-30) REVERT: C 73 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8638 (tm-30) REVERT: C 96 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7374 (tm-30) REVERT: C 107 GLU cc_start: 0.8927 (pt0) cc_final: 0.8644 (pp20) REVERT: C 124 LYS cc_start: 0.9309 (pttp) cc_final: 0.8903 (pttp) REVERT: D 44 LYS cc_start: 0.9500 (mmtm) cc_final: 0.9265 (mmtm) REVERT: D 63 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 64 ASN cc_start: 0.9285 (m-40) cc_final: 0.8902 (m-40) REVERT: D 68 ASP cc_start: 0.8696 (m-30) cc_final: 0.8421 (m-30) REVERT: D 92 ARG cc_start: 0.8694 (tpt90) cc_final: 0.8430 (tpt90) REVERT: E 87 GLN cc_start: 0.9380 (tt0) cc_final: 0.8743 (mt0) REVERT: E 89 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8174 (tp-100) REVERT: G 101 PHE cc_start: 0.9401 (t80) cc_final: 0.8901 (t80) REVERT: G 131 ARG cc_start: 0.9388 (ptm-80) cc_final: 0.9124 (ptm-80) REVERT: H 31 LYS cc_start: 0.9619 (ptpp) cc_final: 0.9361 (pttm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1110 time to fit residues: 21.2612 Evaluate side-chains 115 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.045052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.033999 restraints weight = 83092.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034926 restraints weight = 45686.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035549 restraints weight = 31363.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035920 restraints weight = 24758.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036179 restraints weight = 21478.587| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2324 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= 0.150 Angle : 0.702 9.646 14265 Z= 0.406 Chirality : 0.046 0.241 1636 Planarity : 0.005 0.060 1016 Dihedral : 33.070 179.650 3157 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 1.26 (0.34), residues: 558 helix: 1.62 (0.24), residues: 423 sheet: None (None), residues: 0 loop : -1.71 (0.45), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 118 TYR 0.026 0.002 TYR E 110 PHE 0.021 0.002 PHE C 78 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 0.00256 / 0.15 ( 9844) covalent geometry : angle 0.70218 / 0.41 (14265) hydrogen bonds : bond 0.04845 / 3.25 ( 581) hydrogen bonds : angle 3.26402 / 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 151 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.159 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: 0.7861 (mt-10) cc_final: 0.7151 (mp0) REVERT: A 107 GLU cc_start: 0.9111 (pt0) cc_final: 0.8732 (pt0) REVERT: A 110 TYR cc_start: 0.9115 (t80) cc_final: 0.8840 (t80) REVERT: B 44 LYS cc_start: 0.9087 (mmpt) cc_final: 0.8676 (mmmt) REVERT: B 59 LYS cc_start: 0.9710 (tmtt) cc_final: 0.9400 (tptt) REVERT: B 84 MET cc_start: 0.6796 (mmp) cc_final: 0.6170 (mmp) REVERT: B 85 ASP cc_start: 0.7523 (m-30) cc_final: 0.6962 (m-30) REVERT: C 73 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8687 (tm-30) REVERT: C 96 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7379 (tm-30) REVERT: C 107 GLU cc_start: 0.8875 (pt0) cc_final: 0.8586 (pp20) REVERT: C 124 LYS cc_start: 0.9323 (pttp) cc_final: 0.8899 (pttp) REVERT: D 44 LYS cc_start: 0.9499 (mmtm) cc_final: 0.9067 (mmtt) REVERT: D 63 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8130 (tm-30) REVERT: D 67 ARG cc_start: 0.8990 (ttp-170) cc_final: 0.8622 (ttp80) REVERT: D 68 ASP cc_start: 0.8620 (m-30) cc_final: 0.8311 (m-30) REVERT: E 87 GLN cc_start: 0.9418 (tt0) cc_final: 0.8811 (mt0) REVERT: E 89 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8096 (tp-100) REVERT: F 31 LYS cc_start: 0.9425 (mttm) cc_final: 0.9142 (mtpp) REVERT: F 50 ILE cc_start: 0.9466 (tp) cc_final: 0.8904 (mm) REVERT: G 101 PHE cc_start: 0.9370 (t80) cc_final: 0.8856 (t80) REVERT: G 107 GLU cc_start: 0.9253 (pt0) cc_final: 0.8858 (pp20) REVERT: G 108 ASP cc_start: 0.8630 (m-30) cc_final: 0.7441 (m-30) REVERT: G 131 ARG cc_start: 0.9392 (ptm-80) cc_final: 0.9158 (ptm-80) REVERT: H 49 LEU cc_start: 0.9255 (tp) cc_final: 0.8845 (tp) REVERT: H 67 ARG cc_start: 0.9565 (tpp80) cc_final: 0.9284 (mmt180) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1154 time to fit residues: 22.8729 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 : 0.174 ------------------------------------------------------------------------------- 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: 4.9990 chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.044887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.033900 restraints weight = 84553.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.034832 restraints weight = 46462.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035452 restraints weight = 31937.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035829 restraints weight = 25145.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036094 restraints weight = 21764.460| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2475 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= 0.159 Angle : 0.702 10.194 14265 Z= 0.405 Chirality : 0.045 0.242 1636 Planarity : 0.005 0.065 1016 Dihedral : 33.025 179.303 3157 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 1.42 (0.34), residues: 558 helix: 1.73 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.62 (0.45), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 118 TYR 0.020 0.002 TYR E 110 PHE 0.022 0.002 PHE C 78 TRP 0.007 0.001 TRP E 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 ( 9844) covalent geometry : angle 0.70246 / 0.40 (14265) hydrogen bonds : bond 0.05257 / 3.50 ( 581) hydrogen bonds : angle 3.29168 / 2.43 ( 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 152 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.187 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 67 PHE cc_start: 0.8388 (t80) cc_final: 0.8071 (t80) REVERT: A 99 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7325 (mp0) REVERT: A 107 GLU cc_start: 0.9099 (pt0) cc_final: 0.8689 (pt0) REVERT: A 110 TYR cc_start: 0.9120 (t80) cc_final: 0.8841 (t80) REVERT: B 44 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8660 (mmmt) REVERT: B 59 LYS cc_start: 0.9709 (tmtt) cc_final: 0.9392 (tptt) REVERT: B 84 MET cc_start: 0.6796 (mmp) cc_final: 0.6135 (mmp) REVERT: B 85 ASP cc_start: 0.7568 (m-30) cc_final: 0.6916 (m-30) REVERT: C 73 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 96 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 107 GLU cc_start: 0.8900 (pt0) cc_final: 0.8590 (pp20) REVERT: D 44 LYS cc_start: 0.9496 (mmtm) cc_final: 0.9061 (mmtt) REVERT: D 53 GLU cc_start: 0.8971 (tp30) cc_final: 0.8666 (tp30) REVERT: D 63 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8122 (tm-30) REVERT: D 67 ARG cc_start: 0.8970 (ttp-170) cc_final: 0.8601 (ttp80) REVERT: D 68 ASP cc_start: 0.8576 (m-30) cc_final: 0.8245 (m-30) REVERT: E 87 GLN cc_start: 0.9407 (tt0) cc_final: 0.8815 (mt0) REVERT: E 89 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8097 (tp-100) REVERT: E 96 GLU cc_start: 0.9000 (tp30) cc_final: 0.8670 (tp30) REVERT: F 50 ILE cc_start: 0.9416 (tp) cc_final: 0.9079 (tp) REVERT: G 101 PHE cc_start: 0.9388 (t80) cc_final: 0.8881 (t80) REVERT: G 107 GLU cc_start: 0.9270 (pt0) cc_final: 0.8870 (pp20) REVERT: G 108 ASP cc_start: 0.8767 (m-30) cc_final: 0.7470 (m-30) REVERT: G 131 ARG cc_start: 0.9393 (ptm-80) cc_final: 0.9160 (ptm-80) REVERT: H 49 LEU cc_start: 0.9239 (tp) cc_final: 0.8747 (tp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1114 time to fit residues: 22.1617 Evaluate side-chains 121 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 5 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.045160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.034114 restraints weight = 83991.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.035047 restraints weight = 46339.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035631 restraints weight = 32042.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036034 restraints weight = 25413.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036209 restraints weight = 21984.108| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9844 Z= 0.145 Angle : 0.696 10.022 14265 Z= 0.400 Chirality : 0.045 0.244 1636 Planarity : 0.004 0.061 1016 Dihedral : 32.999 179.195 3157 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.53 (0.34), residues: 558 helix: 1.81 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.57 (0.44), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 131 TYR 0.022 0.002 TYR E 110 PHE 0.020 0.002 PHE D 61 TRP 0.007 0.001 TRP E 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 ( 9844) covalent geometry : angle 0.69627 / 0.40 (14265) hydrogen bonds : bond 0.04680 / 3.12 ( 581) hydrogen bonds : angle 3.26644 / 2.42 ( 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 152 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.220 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 67 PHE cc_start: 0.8435 (t80) cc_final: 0.8055 (t80) REVERT: A 69 ARG cc_start: 0.8086 (pmt-80) cc_final: 0.7661 (pmt-80) REVERT: A 99 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7320 (mp0) REVERT: A 107 GLU cc_start: 0.9093 (pt0) cc_final: 0.8687 (pt0) REVERT: A 110 TYR cc_start: 0.9102 (t80) cc_final: 0.8850 (t80) REVERT: B 44 LYS cc_start: 0.9049 (mmpt) cc_final: 0.8651 (mmmt) REVERT: B 59 LYS cc_start: 0.9711 (tmtt) cc_final: 0.9407 (tptt) REVERT: B 84 MET cc_start: 0.6797 (mmp) cc_final: 0.6126 (mmp) REVERT: B 85 ASP cc_start: 0.7525 (m-30) cc_final: 0.6882 (m-30) REVERT: C 73 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8604 (tm-30) REVERT: C 96 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 107 GLU cc_start: 0.8884 (pt0) cc_final: 0.8570 (pp20) REVERT: D 44 LYS cc_start: 0.9490 (mmtm) cc_final: 0.9221 (mmtm) REVERT: D 53 GLU cc_start: 0.8935 (tp30) cc_final: 0.8660 (tp30) REVERT: D 63 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 67 ARG cc_start: 0.8974 (ttp-170) cc_final: 0.8607 (ttp80) REVERT: D 68 ASP cc_start: 0.8599 (m-30) cc_final: 0.8270 (m-30) REVERT: E 87 GLN cc_start: 0.9397 (tt0) cc_final: 0.8954 (mt0) REVERT: E 89 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8038 (tp-100) REVERT: E 96 GLU cc_start: 0.8977 (tp30) cc_final: 0.8603 (tp30) REVERT: E 130 ARG cc_start: 0.8921 (ttt90) cc_final: 0.8615 (tpt-90) REVERT: F 31 LYS cc_start: 0.9442 (mttm) cc_final: 0.9143 (mtpp) REVERT: F 50 ILE cc_start: 0.9318 (tp) cc_final: 0.9017 (tp) REVERT: G 101 PHE cc_start: 0.9380 (t80) cc_final: 0.8881 (t80) REVERT: G 107 GLU cc_start: 0.9199 (pt0) cc_final: 0.8814 (pp20) REVERT: G 108 ASP cc_start: 0.8641 (m-30) cc_final: 0.7406 (m-30) REVERT: G 131 ARG cc_start: 0.9364 (ptm-80) cc_final: 0.9138 (ptm-80) REVERT: H 49 LEU cc_start: 0.9219 (tp) cc_final: 0.8660 (tp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1191 time to fit residues: 23.5876 Evaluate side-chains 121 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.045180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034225 restraints weight = 83347.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.035157 restraints weight = 46074.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035753 restraints weight = 31855.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036138 restraints weight = 25243.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036403 restraints weight = 21824.590| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2675 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= 0.151 Angle : 0.698 8.789 14265 Z= 0.403 Chirality : 0.045 0.246 1636 Planarity : 0.004 0.043 1016 Dihedral : 32.979 178.829 3157 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 1.63 (0.34), residues: 558 helix: 1.89 (0.24), residues: 420 sheet: None (None), residues: 0 loop : -1.51 (0.44), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 131 TYR 0.027 0.002 TYR E 110 PHE 0.020 0.002 PHE D 61 TRP 0.006 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 ( 9844) covalent geometry : angle 0.69831 / 0.40 (14265) hydrogen bonds : bond 0.04867 / 3.24 ( 581) hydrogen bonds : angle 3.24679 / 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 : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8390 (t80) cc_final: 0.8087 (t80) REVERT: A 99 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7348 (mp0) REVERT: A 107 GLU cc_start: 0.9096 (pt0) cc_final: 0.8681 (pt0) REVERT: A 110 TYR cc_start: 0.9094 (t80) cc_final: 0.8857 (t80) REVERT: B 44 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8576 (mmmt) REVERT: B 84 MET cc_start: 0.6768 (mmp) cc_final: 0.6107 (mmp) REVERT: B 85 ASP cc_start: 0.7567 (m-30) cc_final: 0.6885 (m-30) REVERT: C 73 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 96 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7409 (tm-30) REVERT: C 107 GLU cc_start: 0.8885 (pt0) cc_final: 0.8579 (pp20) REVERT: D 44 LYS cc_start: 0.9486 (mmtm) cc_final: 0.9033 (mmtt) REVERT: D 53 GLU cc_start: 0.8995 (tp30) cc_final: 0.8687 (tp30) REVERT: D 63 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8106 (tm-30) REVERT: D 67 ARG cc_start: 0.8965 (ttp-170) cc_final: 0.8661 (ttp80) REVERT: D 68 ASP cc_start: 0.8614 (m-30) cc_final: 0.8274 (m-30) REVERT: E 87 GLN cc_start: 0.9405 (tt0) cc_final: 0.9112 (mt0) REVERT: E 89 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8036 (tp-100) REVERT: E 96 GLU cc_start: 0.8975 (tp30) cc_final: 0.8615 (tp30) REVERT: F 31 LYS cc_start: 0.9407 (mttm) cc_final: 0.9131 (mtpp) REVERT: F 82 THR cc_start: 0.9182 (m) cc_final: 0.8831 (p) REVERT: G 101 PHE cc_start: 0.9358 (t80) cc_final: 0.8822 (t80) REVERT: G 107 GLU cc_start: 0.9238 (pt0) cc_final: 0.8891 (pp20) REVERT: G 108 ASP cc_start: 0.8788 (m-30) cc_final: 0.7493 (m-30) REVERT: G 110 TYR cc_start: 0.9347 (t80) cc_final: 0.9021 (t80) REVERT: H 49 LEU cc_start: 0.9197 (tp) cc_final: 0.8694 (tp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1176 time to fit residues: 23.1279 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 : 0.247 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.043953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.033244 restraints weight = 82726.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034148 restraints weight = 46086.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.034721 restraints weight = 31820.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035109 restraints weight = 25158.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035372 restraints weight = 21637.528| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2866 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= 0.199 Angle : 0.740 8.633 14265 Z= 0.424 Chirality : 0.046 0.245 1636 Planarity : 0.005 0.056 1016 Dihedral : 33.067 178.323 3157 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 1.76 (0.24), residues: 420 sheet: None (None), residues: 0 loop : -1.52 (0.44), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 131 TYR 0.023 0.002 TYR E 110 PHE 0.023 0.002 PHE H 61 TRP 0.004 0.001 TRP E 86 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.20 ( 9844) covalent geometry : angle 0.73973 / 0.42 (14265) hydrogen bonds : bond 0.06290 / 4.19 ( 581) hydrogen bonds : angle 3.46217 / 2.58 ( 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 146 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8473 (t80) cc_final: 0.8136 (t80) REVERT: A 99 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 107 GLU cc_start: 0.9101 (pt0) cc_final: 0.8692 (pt0) REVERT: A 110 TYR cc_start: 0.9102 (t80) cc_final: 0.8859 (t80) REVERT: B 44 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8593 (mmmt) REVERT: B 59 LYS cc_start: 0.9717 (tmtt) cc_final: 0.9364 (tmtt) REVERT: B 84 MET cc_start: 0.7116 (mmp) cc_final: 0.6886 (mmp) REVERT: B 85 ASP cc_start: 0.7526 (m-30) cc_final: 0.6917 (m-30) REVERT: C 73 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8621 (tm-30) REVERT: C 96 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 107 GLU cc_start: 0.8900 (pt0) cc_final: 0.8580 (pp20) REVERT: D 44 LYS cc_start: 0.9501 (mmtm) cc_final: 0.9203 (mmtm) REVERT: D 53 GLU cc_start: 0.9054 (tp30) cc_final: 0.8755 (tp30) REVERT: D 63 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8134 (tm-30) REVERT: D 67 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8688 (ttp80) REVERT: D 68 ASP cc_start: 0.8648 (m-30) cc_final: 0.8441 (m-30) REVERT: D 92 ARG cc_start: 0.8803 (tmt170) cc_final: 0.8515 (ttt-90) REVERT: E 87 GLN cc_start: 0.9412 (tt0) cc_final: 0.9032 (mt0) REVERT: E 89 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8105 (tp-100) REVERT: E 96 GLU cc_start: 0.9033 (tp30) cc_final: 0.8797 (tp30) REVERT: F 92 ARG cc_start: 0.8381 (tpt-90) cc_final: 0.7954 (tpt-90) REVERT: G 101 PHE cc_start: 0.9390 (t80) cc_final: 0.8941 (t80) REVERT: G 107 GLU cc_start: 0.9230 (pt0) cc_final: 0.8827 (pp20) REVERT: G 108 ASP cc_start: 0.8759 (m-30) cc_final: 0.7473 (m-30) REVERT: G 110 TYR cc_start: 0.9364 (t80) cc_final: 0.9079 (t80) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1232 time to fit residues: 23.5312 Evaluate side-chains 114 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 = 0.044166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.033363 restraints weight = 82686.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.034271 restraints weight = 46049.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.034868 restraints weight = 31808.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035255 restraints weight = 25142.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035514 restraints weight = 21647.912| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9844 Z= 0.171 Angle : 0.735 11.920 14265 Z= 0.417 Chirality : 0.046 0.244 1636 Planarity : 0.004 0.035 1016 Dihedral : 33.138 178.349 3157 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.34), residues: 558 helix: 1.84 (0.24), residues: 420 sheet: None (None), residues: 0 loop : -1.51 (0.44), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 131 TYR 0.024 0.002 TYR E 110 PHE 0.023 0.002 PHE D 61 TRP 0.005 0.001 TRP E 86 HIS 0.004 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 ( 9844) covalent geometry : angle 0.73541 / 0.42 (14265) hydrogen bonds : bond 0.05231 / 3.47 ( 581) hydrogen bonds : angle 3.41639 / 2.55 ( 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 150 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.167 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 67 PHE cc_start: 0.8506 (t80) cc_final: 0.8163 (t80) REVERT: A 99 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 107 GLU cc_start: 0.9094 (pt0) cc_final: 0.8677 (pt0) REVERT: A 110 TYR cc_start: 0.9087 (t80) cc_final: 0.8855 (t80) REVERT: B 44 LYS cc_start: 0.9064 (mmpt) cc_final: 0.8670 (mmmt) REVERT: B 59 LYS cc_start: 0.9715 (tmtt) cc_final: 0.9424 (tptt) REVERT: B 84 MET cc_start: 0.7233 (mmp) cc_final: 0.6961 (mmp) REVERT: B 85 ASP cc_start: 0.7613 (m-30) cc_final: 0.6954 (m-30) REVERT: C 73 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8610 (tm-30) REVERT: C 96 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7512 (tm-30) REVERT: C 107 GLU cc_start: 0.8890 (pt0) cc_final: 0.8587 (pp20) REVERT: C 130 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8662 (tpt90) REVERT: D 44 LYS cc_start: 0.9495 (mmtm) cc_final: 0.9208 (mmtm) REVERT: D 53 GLU cc_start: 0.9052 (tp30) cc_final: 0.8754 (tp30) REVERT: D 63 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8143 (tm-30) REVERT: D 67 ARG cc_start: 0.9005 (ttp-170) cc_final: 0.8666 (ttp80) REVERT: E 87 GLN cc_start: 0.9401 (tt0) cc_final: 0.9048 (mt0) REVERT: E 89 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8060 (tp-100) REVERT: G 101 PHE cc_start: 0.9369 (t80) cc_final: 0.8916 (t80) REVERT: G 107 GLU cc_start: 0.9235 (pt0) cc_final: 0.8913 (pp20) REVERT: G 110 TYR cc_start: 0.9355 (t80) cc_final: 0.9094 (t80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1144 time to fit residues: 22.4660 Evaluate side-chains 114 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.0170 chunk 63 optimal weight: 30.0000 chunk 64 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.5622 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.044268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.033510 restraints weight = 81437.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034414 restraints weight = 45563.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035027 restraints weight = 31634.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035398 restraints weight = 24941.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.035661 restraints weight = 21514.199| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3074 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= 0.160 Angle : 0.733 10.832 14265 Z= 0.416 Chirality : 0.046 0.246 1636 Planarity : 0.004 0.049 1016 Dihedral : 33.131 178.287 3157 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.34), residues: 558 helix: 1.71 (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 0.024 0.002 TYR E 110 PHE 0.022 0.002 PHE D 61 TRP 0.006 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 ( 9844) covalent geometry : angle 0.73260 / 0.42 (14265) hydrogen bonds : bond 0.05141 / 3.39 ( 581) hydrogen bonds : angle 3.41067 / 2.55 ( 1470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1451.44 seconds wall clock time: 25 minutes 46.28 seconds (1546.28 seconds total)