Starting phenix.real_space_refine on Wed Aug 5 19:54:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbx_36148/08_2026/8jbx_36148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbx_36148/08_2026/8jbx_36148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2026/8jbx_36148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2026/8jbx_36148_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2026/8jbx_36148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2026/8jbx_36148.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 288 5.49 5 S 14 5.16 5 C 6564 2.51 5 N 2227 2.21 5 O 2788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 11881 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.36, per 1000 atoms: 0.20 Number of scatterers: 11881 At special positions: 0 Unit cell: (75.26, 118.72, 117.66, 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 14 16.00 P 288 15.00 O 2788 8.00 N 2227 7.00 C 6564 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: 0.90 Conformation dependent library (CDL) restraints added in 266.3 milliseconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 72.7% alpha, 2.7% beta 142 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.751A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.644A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.300A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.422A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.832A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.554A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.522A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.692A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.629A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.330A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 38 through 49 removed outlier: 3.612A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 83 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.422A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.390A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.712A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.252A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.525A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 403 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2342 1.33 - 1.45: 4166 1.45 - 1.57: 5576 1.57 - 1.69: 576 1.69 - 1.81: 24 Bond restraints: 12684 Sorted by residual: bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.28e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" CA ASP F 85 " pdb=" C ASP F 85 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.26e-02 6.30e+03 1.14e+01 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 ... (remaining 12679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 17370 1.64 - 3.29: 949 3.29 - 4.93: 42 4.93 - 6.57: 9 6.57 - 8.21: 3 Bond angle restraints: 18373 Sorted by residual: angle pdb=" N ASP F 85 " pdb=" CA ASP F 85 " pdb=" C ASP F 85 " ideal model delta sigma weight residual 111.14 104.13 7.01 1.08e+00 8.57e-01 4.21e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " 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 J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I -59 " pdb=" C4 DT I -59 " pdb=" O4 DT I -59 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 18368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 5445 35.60 - 71.19: 1419 71.19 - 106.78: 11 106.78 - 142.38: 3 142.38 - 177.97: 1 Dihedral angle restraints: 6879 sinusoidal: 4707 harmonic: 2172 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 37.97 -177.97 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 87.58 132.42 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" C4' DA J -38 " pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 92.19 127.81 1 3.50e+01 8.16e-04 1.26e+01 ... (remaining 6876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1214 0.033 - 0.066: 600 0.066 - 0.099: 191 0.099 - 0.132: 79 0.132 - 0.164: 6 Chirality restraints: 2090 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" C3' DC I 4 " pdb=" C4' DC I 4 " pdb=" O3' DC I 4 " pdb=" C2' DC I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2087 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 84 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C MET F 84 " -0.054 2.00e-02 2.50e+03 pdb=" O MET F 84 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP F 85 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 49 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO D 50 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.001 2.00e-02 2.50e+03 1.28e-02 3.28e+00 pdb=" CG TYR F 88 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " -0.014 2.00e-02 2.50e+03 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2028 2.77 - 3.31: 10993 3.31 - 3.84: 24017 3.84 - 4.37: 26289 4.37 - 4.90: 38419 Nonbonded interactions: 101746 Sorted by model distance: nonbonded pdb=" NH1 ARG C 81 " pdb=" O GLY C 106 " model vdw 2.242 3.120 nonbonded pdb=" NH2 ARG F 92 " pdb=" OE1 GLU H 76 " model vdw 2.245 3.120 nonbonded pdb=" O SER D 124 " pdb=" OG SER D 124 " model vdw 2.249 3.040 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DT I -42 " model vdw 2.266 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE2 GLU E 133 " model vdw 2.279 3.040 ... (remaining 101741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.620 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 0.080 12684 Z= 0.516 Angle : 0.752 8.214 18373 Z= 0.656 Chirality : 0.044 0.164 2090 Planarity : 0.004 0.070 1320 Dihedral : 28.645 177.973 5479 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.48 % Allowed : 30.83 % Favored : 68.69 % 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: 1.72 (0.32), residues: 734 helix: 1.91 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -1.08 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.024 0.002 TYR D 121 PHE 0.007 0.001 PHE E 78 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.52 (12684) covalent geometry : angle 0.75157 / 0.66 (18373) hydrogen bonds : bond 0.09436 / 6.57 ( 767) hydrogen bonds : angle 3.58959 / 2.49 ( 1931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 269 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 87 SER cc_start: 0.9548 (p) cc_final: 0.9231 (t) REVERT: A 94 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8435 (tp30) REVERT: A 125 GLN cc_start: 0.9096 (mt0) cc_final: 0.8832 (mt0) REVERT: D 42 TYR cc_start: 0.7666 (t80) cc_final: 0.7155 (t80) REVERT: D 68 ASP cc_start: 0.9156 (t0) cc_final: 0.8906 (t0) REVERT: D 89 ILE cc_start: 0.9181 (mm) cc_final: 0.8866 (mm) REVERT: E 74 ILE cc_start: 0.9535 (tt) cc_final: 0.9302 (tt) REVERT: E 76 GLN cc_start: 0.9055 (pp30) cc_final: 0.8822 (pp30) REVERT: E 108 ASN cc_start: 0.9476 (t0) cc_final: 0.9140 (t0) REVERT: F 63 GLU cc_start: 0.8866 (tt0) cc_final: 0.8620 (mt-10) REVERT: F 80 THR cc_start: 0.9432 (t) cc_final: 0.8999 (p) REVERT: G 35 ARG cc_start: 0.9079 (mtm110) cc_final: 0.8755 (mtm-85) REVERT: G 59 THR cc_start: 0.9519 (m) cc_final: 0.9302 (t) REVERT: G 71 ARG cc_start: 0.9184 (ttp-110) cc_final: 0.8769 (ttp-110) REVERT: G 100 VAL cc_start: 0.9353 (t) cc_final: 0.9109 (p) REVERT: G 101 THR cc_start: 0.9279 (m) cc_final: 0.8909 (t) REVERT: H 45 LEU cc_start: 0.9633 (tp) cc_final: 0.9384 (tt) REVERT: H 113 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8181 (tm-30) outliers start: 3 outliers final: 0 residues processed: 270 average time/residue: 0.1236 time to fit residues: 44.5893 Evaluate side-chains 223 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 63 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.043028 restraints weight = 46225.898| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.42 r_work: 0.2619 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12684 Z= 0.225 Angle : 0.698 9.504 18373 Z= 0.403 Chirality : 0.044 0.251 2090 Planarity : 0.005 0.057 1320 Dihedral : 30.943 175.459 3997 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.67 % Allowed : 28.43 % Favored : 67.89 % 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: 1.70 (0.31), residues: 734 helix: 1.94 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.12 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 33 TYR 0.018 0.002 TYR C 39 PHE 0.013 0.001 PHE E 104 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (12684) covalent geometry : angle 0.69843 / 0.40 (18373) hydrogen bonds : bond 0.05091 / 3.52 ( 767) hydrogen bonds : angle 3.16579 / 2.26 ( 1931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.273 Fit side-chains REVERT: A 76 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 87 SER cc_start: 0.9398 (p) cc_final: 0.9155 (t) REVERT: A 94 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8599 (tp30) REVERT: A 108 ASN cc_start: 0.9398 (t0) cc_final: 0.9189 (t0) REVERT: B 27 GLN cc_start: 0.8633 (pt0) cc_final: 0.8362 (pm20) REVERT: B 31 LYS cc_start: 0.9408 (tttt) cc_final: 0.9033 (tttp) REVERT: B 53 GLU cc_start: 0.8760 (tp30) cc_final: 0.8071 (tp30) REVERT: B 84 MET cc_start: 0.8931 (tpp) cc_final: 0.8423 (tpt) REVERT: C 99 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8633 (tpp80) REVERT: D 42 TYR cc_start: 0.7868 (t80) cc_final: 0.7463 (t80) REVERT: D 47 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8837 (tm-30) REVERT: D 68 ASP cc_start: 0.9155 (t0) cc_final: 0.8800 (t0) REVERT: D 79 ARG cc_start: 0.9295 (mtm180) cc_final: 0.9088 (ttp-110) REVERT: D 89 ILE cc_start: 0.8923 (mm) cc_final: 0.8693 (mm) REVERT: D 105 GLU cc_start: 0.9011 (tp30) cc_final: 0.8266 (tp30) REVERT: E 42 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7983 (ttm110) REVERT: E 74 ILE cc_start: 0.9182 (tt) cc_final: 0.8931 (tt) REVERT: E 76 GLN cc_start: 0.9176 (pp30) cc_final: 0.8867 (pp30) REVERT: E 108 ASN cc_start: 0.9529 (t0) cc_final: 0.9225 (t0) REVERT: F 53 GLU cc_start: 0.9163 (tp30) cc_final: 0.8897 (tp30) REVERT: F 63 GLU cc_start: 0.9158 (tt0) cc_final: 0.8860 (mt-10) REVERT: F 85 ASP cc_start: 0.8962 (m-30) cc_final: 0.8756 (m-30) REVERT: G 59 THR cc_start: 0.9329 (m) cc_final: 0.9030 (t) REVERT: G 100 VAL cc_start: 0.9666 (t) cc_final: 0.9143 (p) REVERT: G 101 THR cc_start: 0.9077 (m) cc_final: 0.8577 (t) REVERT: H 33 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8037 (mmm-85) REVERT: H 105 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8249 (mm-30) REVERT: H 113 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8383 (tm-30) outliers start: 23 outliers final: 13 residues processed: 240 average time/residue: 0.1105 time to fit residues: 36.3485 Evaluate side-chains 226 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.0170 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043808 restraints weight = 46351.675| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.46 r_work: 0.2647 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12684 Z= 0.157 Angle : 0.636 7.642 18373 Z= 0.376 Chirality : 0.042 0.242 2090 Planarity : 0.004 0.049 1320 Dihedral : 31.046 176.289 3997 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.51 % Allowed : 27.48 % Favored : 69.01 % 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: 1.81 (0.31), residues: 734 helix: 2.03 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.11 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.020 0.002 TYR C 39 PHE 0.008 0.001 PHE E 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (12684) covalent geometry : angle 0.63629 / 0.38 (18373) hydrogen bonds : bond 0.04465 / 3.10 ( 767) hydrogen bonds : angle 3.00783 / 2.17 ( 1931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8770 (tm-30) REVERT: A 87 SER cc_start: 0.9376 (p) cc_final: 0.9136 (t) REVERT: A 94 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8584 (tp30) REVERT: B 27 GLN cc_start: 0.8581 (pt0) cc_final: 0.8294 (pm20) REVERT: B 31 LYS cc_start: 0.9428 (tttt) cc_final: 0.9098 (tttp) REVERT: B 53 GLU cc_start: 0.8663 (tp30) cc_final: 0.8044 (tp30) REVERT: B 84 MET cc_start: 0.8927 (tpp) cc_final: 0.8475 (tpt) REVERT: B 92 ARG cc_start: 0.9469 (ttp80) cc_final: 0.9019 (ttp80) REVERT: C 38 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8296 (p0) REVERT: C 56 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8673 (tm-30) REVERT: C 99 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8677 (tpp80) REVERT: D 42 TYR cc_start: 0.7791 (t80) cc_final: 0.7423 (t80) REVERT: D 47 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8867 (tm-30) REVERT: D 57 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8217 (mmmm) REVERT: D 68 ASP cc_start: 0.9131 (t0) cc_final: 0.8776 (t0) REVERT: D 86 ARG cc_start: 0.8937 (mmt90) cc_final: 0.8582 (mmt90) REVERT: D 89 ILE cc_start: 0.8828 (mm) cc_final: 0.8561 (mm) REVERT: D 105 GLU cc_start: 0.8955 (tp30) cc_final: 0.8188 (tp30) REVERT: E 42 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8072 (ttm110) REVERT: E 61 LEU cc_start: 0.8939 (mt) cc_final: 0.8729 (mp) REVERT: E 74 ILE cc_start: 0.9196 (tt) cc_final: 0.8937 (tt) REVERT: E 76 GLN cc_start: 0.9135 (pp30) cc_final: 0.8800 (pp30) REVERT: F 53 GLU cc_start: 0.9130 (tp30) cc_final: 0.8919 (tp30) REVERT: F 63 GLU cc_start: 0.9131 (tt0) cc_final: 0.8841 (mt-10) REVERT: F 85 ASP cc_start: 0.9039 (m-30) cc_final: 0.8838 (m-30) REVERT: G 24 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8707 (mm110) REVERT: G 59 THR cc_start: 0.9300 (m) cc_final: 0.9053 (t) REVERT: G 90 ASP cc_start: 0.7951 (t0) cc_final: 0.7553 (t0) REVERT: G 91 GLU cc_start: 0.8673 (tp30) cc_final: 0.8409 (tp30) REVERT: G 92 GLU cc_start: 0.9304 (mp0) cc_final: 0.8973 (tt0) REVERT: G 101 THR cc_start: 0.9044 (m) cc_final: 0.8450 (t) REVERT: H 33 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8071 (mmm-85) REVERT: H 68 ASP cc_start: 0.9043 (t0) cc_final: 0.8833 (t0) REVERT: H 113 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8401 (tm-30) outliers start: 22 outliers final: 13 residues processed: 257 average time/residue: 0.0994 time to fit residues: 34.8393 Evaluate side-chains 235 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 68 GLN E 93 GLN E 108 ASN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044225 restraints weight = 46330.906| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.45 r_work: 0.2652 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12684 Z= 0.158 Angle : 0.636 7.232 18373 Z= 0.374 Chirality : 0.042 0.244 2090 Planarity : 0.004 0.049 1320 Dihedral : 31.091 175.807 3997 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 3.04 % Allowed : 29.87 % Favored : 67.09 % 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: 1.80 (0.31), residues: 734 helix: 1.92 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.95 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.019 0.002 TYR D 40 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (12684) covalent geometry : angle 0.63622 / 0.37 (18373) hydrogen bonds : bond 0.04340 / 3.00 ( 767) hydrogen bonds : angle 3.04828 / 2.18 ( 1931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 87 SER cc_start: 0.9364 (p) cc_final: 0.9121 (t) REVERT: A 94 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8593 (tp30) REVERT: B 27 GLN cc_start: 0.8599 (pt0) cc_final: 0.8315 (pm20) REVERT: B 31 LYS cc_start: 0.9462 (tttt) cc_final: 0.9120 (tttp) REVERT: B 53 GLU cc_start: 0.8600 (tp30) cc_final: 0.8018 (tp30) REVERT: B 84 MET cc_start: 0.8905 (tpp) cc_final: 0.8562 (tpp) REVERT: B 88 TYR cc_start: 0.8489 (t80) cc_final: 0.7922 (t80) REVERT: B 92 ARG cc_start: 0.9497 (ttp80) cc_final: 0.8978 (ttp80) REVERT: B 98 TYR cc_start: 0.9289 (m-10) cc_final: 0.8971 (m-10) REVERT: C 61 GLU cc_start: 0.8669 (tt0) cc_final: 0.8293 (tt0) REVERT: C 64 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9004 (pp20) REVERT: D 42 TYR cc_start: 0.7813 (t80) cc_final: 0.7478 (t80) REVERT: D 47 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8874 (tm-30) REVERT: D 57 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8212 (mmmm) REVERT: D 68 ASP cc_start: 0.9132 (t0) cc_final: 0.8779 (t0) REVERT: D 89 ILE cc_start: 0.8803 (mm) cc_final: 0.8500 (mm) REVERT: D 105 GLU cc_start: 0.8943 (tp30) cc_final: 0.8176 (tp30) REVERT: E 42 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8049 (ttm110) REVERT: E 74 ILE cc_start: 0.9213 (tt) cc_final: 0.8939 (tt) REVERT: E 76 GLN cc_start: 0.9151 (pp30) cc_final: 0.8811 (pp30) REVERT: E 108 ASN cc_start: 0.9535 (t0) cc_final: 0.9169 (t0) REVERT: F 53 GLU cc_start: 0.9127 (tp30) cc_final: 0.8905 (tp30) REVERT: F 63 GLU cc_start: 0.9140 (tt0) cc_final: 0.8848 (mt-10) REVERT: F 72 TYR cc_start: 0.8828 (m-80) cc_final: 0.8589 (m-80) REVERT: G 59 THR cc_start: 0.9312 (m) cc_final: 0.9038 (t) REVERT: G 91 GLU cc_start: 0.8683 (tp30) cc_final: 0.8372 (tp30) REVERT: G 92 GLU cc_start: 0.9326 (mp0) cc_final: 0.9008 (tt0) REVERT: G 100 VAL cc_start: 0.9678 (t) cc_final: 0.9403 (p) REVERT: G 101 THR cc_start: 0.9071 (m) cc_final: 0.8581 (t) REVERT: H 33 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8062 (mmm-85) REVERT: H 68 ASP cc_start: 0.9022 (t0) cc_final: 0.8759 (t0) REVERT: H 113 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8401 (tm-30) outliers start: 19 outliers final: 10 residues processed: 247 average time/residue: 0.1014 time to fit residues: 34.0001 Evaluate side-chains 232 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 30.0000 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 68 GLN F 64 ASN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.059747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.044636 restraints weight = 46117.184| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.47 r_work: 0.2660 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12684 Z= 0.153 Angle : 0.625 7.004 18373 Z= 0.368 Chirality : 0.042 0.243 2090 Planarity : 0.004 0.045 1320 Dihedral : 31.137 175.511 3997 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.88 % Allowed : 30.19 % Favored : 66.93 % 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: 1.81 (0.31), residues: 734 helix: 1.92 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.89 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.028 0.002 TYR D 40 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12684) covalent geometry : angle 0.62549 / 0.37 (18373) hydrogen bonds : bond 0.04234 / 2.92 ( 767) hydrogen bonds : angle 2.99959 / 2.16 ( 1931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8928 (tp) REVERT: A 76 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8768 (tm-30) REVERT: A 87 SER cc_start: 0.9346 (p) cc_final: 0.9105 (t) REVERT: A 94 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8526 (tp30) REVERT: B 27 GLN cc_start: 0.8621 (pt0) cc_final: 0.8346 (pm20) REVERT: B 31 LYS cc_start: 0.9464 (tttt) cc_final: 0.9131 (tttp) REVERT: B 84 MET cc_start: 0.8904 (tpp) cc_final: 0.8499 (tpp) REVERT: B 92 ARG cc_start: 0.9472 (ttp80) cc_final: 0.9029 (ttp80) REVERT: C 36 LYS cc_start: 0.9377 (tppt) cc_final: 0.8999 (tppt) REVERT: C 38 ASN cc_start: 0.8915 (p0) cc_final: 0.8566 (p0) REVERT: C 64 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.9042 (pp20) REVERT: D 42 TYR cc_start: 0.7838 (t80) cc_final: 0.7519 (t80) REVERT: D 47 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8889 (tm-30) REVERT: D 68 ASP cc_start: 0.9145 (t0) cc_final: 0.8789 (t0) REVERT: D 86 ARG cc_start: 0.8922 (mmt90) cc_final: 0.8709 (mtt-85) REVERT: D 89 ILE cc_start: 0.8772 (mm) cc_final: 0.8419 (mm) REVERT: D 105 GLU cc_start: 0.8912 (tp30) cc_final: 0.8315 (tp30) REVERT: E 74 ILE cc_start: 0.9220 (tt) cc_final: 0.8969 (tt) REVERT: E 76 GLN cc_start: 0.9122 (pp30) cc_final: 0.8737 (pp30) REVERT: E 108 ASN cc_start: 0.9507 (t0) cc_final: 0.9165 (t0) REVERT: E 125 GLN cc_start: 0.8746 (mt0) cc_final: 0.8461 (mt0) REVERT: F 63 GLU cc_start: 0.9144 (tt0) cc_final: 0.8847 (mt-10) REVERT: G 24 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8877 (mm-40) REVERT: G 59 THR cc_start: 0.9292 (m) cc_final: 0.9006 (t) REVERT: G 90 ASP cc_start: 0.7902 (t0) cc_final: 0.7524 (t0) REVERT: G 100 VAL cc_start: 0.9664 (t) cc_final: 0.9460 (p) REVERT: G 101 THR cc_start: 0.9072 (m) cc_final: 0.8584 (t) REVERT: H 33 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8108 (mmm-85) REVERT: H 68 ASP cc_start: 0.9005 (t0) cc_final: 0.8786 (t0) REVERT: H 113 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8416 (tm-30) outliers start: 18 outliers final: 11 residues processed: 246 average time/residue: 0.0982 time to fit residues: 33.3690 Evaluate side-chains 235 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 12 optimal weight: 0.5980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 55 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.043063 restraints weight = 46372.247| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.45 r_work: 0.2613 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 12684 Z= 0.219 Angle : 0.681 7.005 18373 Z= 0.388 Chirality : 0.043 0.244 2090 Planarity : 0.004 0.044 1320 Dihedral : 31.302 174.836 3997 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.67 % Allowed : 29.87 % Favored : 66.45 % 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: 1.83 (0.31), residues: 734 helix: 1.89 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.78 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.032 0.002 TYR D 40 PHE 0.006 0.001 PHE B 100 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (12684) covalent geometry : angle 0.68103 / 0.39 (18373) hydrogen bonds : bond 0.04608 / 3.18 ( 767) hydrogen bonds : angle 3.17542 / 2.29 ( 1931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 87 SER cc_start: 0.9371 (p) cc_final: 0.9153 (t) REVERT: A 94 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8647 (tp30) REVERT: B 27 GLN cc_start: 0.8678 (pt0) cc_final: 0.8391 (pm20) REVERT: B 31 LYS cc_start: 0.9464 (tttt) cc_final: 0.9154 (tttp) REVERT: B 53 GLU cc_start: 0.8612 (tp30) cc_final: 0.7984 (tp30) REVERT: B 84 MET cc_start: 0.8960 (tpp) cc_final: 0.8560 (tpp) REVERT: B 88 TYR cc_start: 0.8343 (t80) cc_final: 0.7900 (t80) REVERT: B 92 ARG cc_start: 0.9481 (ttp80) cc_final: 0.9082 (ttp80) REVERT: C 38 ASN cc_start: 0.8947 (p0) cc_final: 0.8600 (p0) REVERT: C 64 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.9048 (pp20) REVERT: D 42 TYR cc_start: 0.7929 (t80) cc_final: 0.7614 (t80) REVERT: D 47 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8907 (tm-30) REVERT: D 68 ASP cc_start: 0.9142 (t0) cc_final: 0.8756 (t0) REVERT: D 89 ILE cc_start: 0.8900 (mm) cc_final: 0.8537 (mm) REVERT: D 105 GLU cc_start: 0.8948 (tp30) cc_final: 0.8326 (tp30) REVERT: E 73 GLU cc_start: 0.8857 (tp30) cc_final: 0.8596 (tp30) REVERT: E 74 ILE cc_start: 0.9227 (tt) cc_final: 0.8927 (tt) REVERT: E 76 GLN cc_start: 0.9133 (pp30) cc_final: 0.8744 (pp30) REVERT: E 108 ASN cc_start: 0.9576 (t0) cc_final: 0.9229 (t0) REVERT: F 63 GLU cc_start: 0.9181 (tt0) cc_final: 0.8716 (mt-10) REVERT: G 24 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8854 (mm110) REVERT: G 35 ARG cc_start: 0.9447 (mtm110) cc_final: 0.8807 (mtm-85) REVERT: G 59 THR cc_start: 0.9317 (m) cc_final: 0.9033 (t) REVERT: G 90 ASP cc_start: 0.8082 (t0) cc_final: 0.7748 (t0) REVERT: G 100 VAL cc_start: 0.9671 (t) cc_final: 0.9350 (p) REVERT: G 101 THR cc_start: 0.9204 (m) cc_final: 0.8635 (p) REVERT: H 33 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8133 (mmm-85) REVERT: H 68 ASP cc_start: 0.9047 (t0) cc_final: 0.8750 (t0) REVERT: H 113 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8402 (tm-30) outliers start: 23 outliers final: 14 residues processed: 233 average time/residue: 0.0970 time to fit residues: 31.0945 Evaluate side-chains 224 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 63 ASN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.059716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044654 restraints weight = 46156.002| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.47 r_work: 0.2657 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12684 Z= 0.149 Angle : 0.629 7.019 18373 Z= 0.369 Chirality : 0.041 0.243 2090 Planarity : 0.004 0.042 1320 Dihedral : 31.228 175.873 3997 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.72 % Allowed : 31.63 % Favored : 65.65 % 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: 1.88 (0.31), residues: 734 helix: 1.95 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.81 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.029 0.002 TYR H 40 PHE 0.010 0.001 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (12684) covalent geometry : angle 0.62917 / 0.37 (18373) hydrogen bonds : bond 0.04133 / 2.85 ( 767) hydrogen bonds : angle 3.03222 / 2.19 ( 1931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8978 (tp) REVERT: A 76 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8726 (tm-30) REVERT: A 87 SER cc_start: 0.9333 (p) cc_final: 0.9092 (t) REVERT: A 90 MET cc_start: 0.8925 (mmt) cc_final: 0.8690 (mmm) REVERT: A 94 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8741 (mm-30) REVERT: B 27 GLN cc_start: 0.8683 (pt0) cc_final: 0.8411 (pm20) REVERT: B 31 LYS cc_start: 0.9470 (tttt) cc_final: 0.9165 (tttp) REVERT: B 53 GLU cc_start: 0.8487 (tp30) cc_final: 0.8067 (tm-30) REVERT: B 84 MET cc_start: 0.9024 (tpp) cc_final: 0.8615 (tpp) REVERT: B 88 TYR cc_start: 0.8149 (t80) cc_final: 0.7910 (t80) REVERT: B 92 ARG cc_start: 0.9435 (ttp80) cc_final: 0.8967 (ttp80) REVERT: C 38 ASN cc_start: 0.8721 (p0) cc_final: 0.8370 (p0) REVERT: C 64 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9027 (pp20) REVERT: C 95 LYS cc_start: 0.9370 (ttmt) cc_final: 0.9017 (tmmt) REVERT: C 99 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8647 (tpp80) REVERT: D 42 TYR cc_start: 0.7834 (t80) cc_final: 0.7618 (t80) REVERT: D 47 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8938 (tm-30) REVERT: D 68 ASP cc_start: 0.9142 (t0) cc_final: 0.8765 (t0) REVERT: D 76 GLU cc_start: 0.9001 (tp30) cc_final: 0.8786 (tp30) REVERT: D 79 ARG cc_start: 0.9150 (ttp-110) cc_final: 0.8815 (ttm-80) REVERT: D 86 ARG cc_start: 0.8980 (mmt90) cc_final: 0.8758 (mtt-85) REVERT: D 105 GLU cc_start: 0.8903 (tp30) cc_final: 0.8245 (tp30) REVERT: E 73 GLU cc_start: 0.8881 (tp30) cc_final: 0.8607 (tp30) REVERT: E 74 ILE cc_start: 0.9230 (tt) cc_final: 0.8933 (tt) REVERT: E 76 GLN cc_start: 0.9104 (pp30) cc_final: 0.8717 (pp30) REVERT: E 108 ASN cc_start: 0.9542 (t0) cc_final: 0.9204 (t0) REVERT: E 125 GLN cc_start: 0.8856 (mt0) cc_final: 0.8613 (mt0) REVERT: F 63 GLU cc_start: 0.9139 (tt0) cc_final: 0.8721 (mt-10) REVERT: F 74 GLU cc_start: 0.9448 (tp30) cc_final: 0.9162 (tp30) REVERT: F 84 MET cc_start: 0.8965 (mmm) cc_final: 0.8619 (mmm) REVERT: G 24 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8861 (mm110) REVERT: G 35 ARG cc_start: 0.9435 (mtm110) cc_final: 0.8797 (mtm-85) REVERT: G 59 THR cc_start: 0.9291 (m) cc_final: 0.9002 (t) REVERT: G 90 ASP cc_start: 0.7969 (t0) cc_final: 0.7473 (t0) REVERT: G 91 GLU cc_start: 0.8650 (tp30) cc_final: 0.8407 (tp30) REVERT: G 92 GLU cc_start: 0.9294 (mp0) cc_final: 0.9003 (tt0) REVERT: G 100 VAL cc_start: 0.9652 (t) cc_final: 0.9413 (p) REVERT: G 101 THR cc_start: 0.9161 (m) cc_final: 0.8576 (p) REVERT: H 33 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8088 (mmm-85) REVERT: H 34 LYS cc_start: 0.8513 (mppt) cc_final: 0.8311 (mtmm) REVERT: H 68 ASP cc_start: 0.9041 (t0) cc_final: 0.8796 (t0) REVERT: H 113 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8461 (tm-30) outliers start: 17 outliers final: 11 residues processed: 248 average time/residue: 0.1027 time to fit residues: 34.7803 Evaluate side-chains 236 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 223 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.041444 restraints weight = 47555.778| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.73 r_work: 0.2543 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12684 Z= 0.228 Angle : 0.700 7.327 18373 Z= 0.394 Chirality : 0.043 0.242 2090 Planarity : 0.004 0.044 1320 Dihedral : 31.359 174.699 3997 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.35 % Allowed : 31.95 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.31), residues: 734 helix: 1.96 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.69 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.041 0.002 TYR D 40 PHE 0.006 0.001 PHE B 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (12684) covalent geometry : angle 0.69993 / 0.39 (18373) hydrogen bonds : bond 0.04628 / 3.20 ( 767) hydrogen bonds : angle 3.15159 / 2.28 ( 1931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 87 SER cc_start: 0.9351 (p) cc_final: 0.9132 (t) REVERT: A 94 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8673 (tp30) REVERT: B 27 GLN cc_start: 0.8778 (pt0) cc_final: 0.8514 (pm20) REVERT: B 31 LYS cc_start: 0.9461 (tttt) cc_final: 0.9167 (tttp) REVERT: B 53 GLU cc_start: 0.8660 (tp30) cc_final: 0.8198 (tm-30) REVERT: B 84 MET cc_start: 0.9041 (tpp) cc_final: 0.8704 (tpp) REVERT: B 92 ARG cc_start: 0.9440 (ttp80) cc_final: 0.9054 (ttp80) REVERT: C 38 ASN cc_start: 0.8877 (p0) cc_final: 0.8516 (p0) REVERT: C 64 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.9058 (pp20) REVERT: D 42 TYR cc_start: 0.7992 (t80) cc_final: 0.7728 (t80) REVERT: D 47 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8921 (tm-30) REVERT: D 68 ASP cc_start: 0.9137 (t0) cc_final: 0.8755 (t0) REVERT: D 76 GLU cc_start: 0.9071 (tp30) cc_final: 0.8830 (tp30) REVERT: D 86 ARG cc_start: 0.9039 (mmt90) cc_final: 0.8797 (mtt-85) REVERT: D 105 GLU cc_start: 0.8949 (tp30) cc_final: 0.8300 (tp30) REVERT: E 73 GLU cc_start: 0.8878 (tp30) cc_final: 0.8613 (tp30) REVERT: E 74 ILE cc_start: 0.9239 (tt) cc_final: 0.8932 (tt) REVERT: E 76 GLN cc_start: 0.9173 (pp30) cc_final: 0.8810 (pp30) REVERT: E 108 ASN cc_start: 0.9574 (t0) cc_final: 0.9250 (t0) REVERT: E 125 GLN cc_start: 0.8951 (mt0) cc_final: 0.8675 (mt0) REVERT: F 63 GLU cc_start: 0.9169 (tt0) cc_final: 0.8798 (mt-10) REVERT: G 24 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8933 (mm110) REVERT: G 59 THR cc_start: 0.9285 (m) cc_final: 0.8966 (t) REVERT: G 90 ASP cc_start: 0.8101 (t0) cc_final: 0.7739 (t0) REVERT: G 100 VAL cc_start: 0.9665 (t) cc_final: 0.9327 (p) REVERT: G 101 THR cc_start: 0.9217 (m) cc_final: 0.8660 (p) REVERT: H 68 ASP cc_start: 0.9051 (t0) cc_final: 0.8760 (t0) REVERT: H 113 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8454 (tm-30) outliers start: 21 outliers final: 15 residues processed: 229 average time/residue: 0.1008 time to fit residues: 31.6983 Evaluate side-chains 226 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 51 optimal weight: 0.0370 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.044266 restraints weight = 46143.022| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.51 r_work: 0.2653 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12684 Z= 0.149 Angle : 0.654 9.861 18373 Z= 0.376 Chirality : 0.042 0.297 2090 Planarity : 0.004 0.055 1320 Dihedral : 31.272 176.011 3997 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.56 % Allowed : 33.07 % Favored : 64.38 % 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: 1.96 (0.31), residues: 734 helix: 1.99 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.69 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 33 TYR 0.034 0.002 TYR D 40 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12684) covalent geometry : angle 0.65437 / 0.38 (18373) hydrogen bonds : bond 0.04061 / 2.79 ( 767) hydrogen bonds : angle 3.06282 / 2.23 ( 1931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 76 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 87 SER cc_start: 0.9325 (p) cc_final: 0.9091 (t) REVERT: A 94 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8649 (tp30) REVERT: B 27 GLN cc_start: 0.8746 (pt0) cc_final: 0.8474 (pm20) REVERT: B 31 LYS cc_start: 0.9451 (tttt) cc_final: 0.9144 (tttp) REVERT: B 53 GLU cc_start: 0.8534 (tp30) cc_final: 0.8150 (tm-30) REVERT: B 92 ARG cc_start: 0.9365 (ttp80) cc_final: 0.9016 (ttp80) REVERT: B 98 TYR cc_start: 0.9290 (m-10) cc_final: 0.9017 (m-10) REVERT: C 38 ASN cc_start: 0.8592 (p0) cc_final: 0.8256 (p0) REVERT: C 64 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9022 (pp20) REVERT: C 95 LYS cc_start: 0.9359 (ttmt) cc_final: 0.9010 (tmmt) REVERT: D 42 TYR cc_start: 0.7860 (t80) cc_final: 0.7655 (t80) REVERT: D 47 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8926 (tm-30) REVERT: D 68 ASP cc_start: 0.9140 (t0) cc_final: 0.8771 (t0) REVERT: D 86 ARG cc_start: 0.8950 (mmt90) cc_final: 0.8727 (mtt-85) REVERT: D 105 GLU cc_start: 0.8903 (tp30) cc_final: 0.8254 (tp30) REVERT: E 73 GLU cc_start: 0.8858 (tp30) cc_final: 0.8590 (tp30) REVERT: E 74 ILE cc_start: 0.9216 (tt) cc_final: 0.8918 (tt) REVERT: E 76 GLN cc_start: 0.9164 (pp30) cc_final: 0.8788 (pp30) REVERT: E 108 ASN cc_start: 0.9548 (t0) cc_final: 0.9220 (t0) REVERT: E 125 GLN cc_start: 0.8874 (mt0) cc_final: 0.8562 (mt0) REVERT: F 63 GLU cc_start: 0.9130 (tt0) cc_final: 0.8682 (mt-10) REVERT: F 84 MET cc_start: 0.9081 (mmm) cc_final: 0.8848 (mmm) REVERT: G 24 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8968 (mm110) REVERT: G 59 THR cc_start: 0.9288 (m) cc_final: 0.9003 (t) REVERT: G 90 ASP cc_start: 0.8045 (t0) cc_final: 0.7562 (t0) REVERT: G 91 GLU cc_start: 0.8650 (tp30) cc_final: 0.8443 (tp30) REVERT: G 92 GLU cc_start: 0.9331 (mp0) cc_final: 0.9013 (tt0) REVERT: G 100 VAL cc_start: 0.9646 (t) cc_final: 0.9379 (p) REVERT: G 101 THR cc_start: 0.9194 (m) cc_final: 0.8587 (p) REVERT: H 68 ASP cc_start: 0.9057 (t0) cc_final: 0.8803 (t0) REVERT: H 71 GLU cc_start: 0.9430 (tm-30) cc_final: 0.9228 (tp30) REVERT: H 113 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8475 (tm-30) outliers start: 16 outliers final: 10 residues processed: 241 average time/residue: 0.1021 time to fit residues: 34.0153 Evaluate side-chains 228 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 78 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043507 restraints weight = 46608.389| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.50 r_work: 0.2630 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12684 Z= 0.183 Angle : 0.687 9.132 18373 Z= 0.387 Chirality : 0.042 0.242 2090 Planarity : 0.004 0.044 1320 Dihedral : 31.323 175.014 3997 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.40 % Allowed : 33.23 % Favored : 64.38 % 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: 1.99 (0.31), residues: 734 helix: 1.99 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.64 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.047 0.003 TYR H 40 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (12684) covalent geometry : angle 0.68700 / 0.39 (18373) hydrogen bonds : bond 0.04252 / 2.93 ( 767) hydrogen bonds : angle 3.12201 / 2.26 ( 1931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8874 (tp) REVERT: A 76 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 87 SER cc_start: 0.9337 (p) cc_final: 0.9109 (t) REVERT: A 94 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8662 (tp30) REVERT: B 27 GLN cc_start: 0.8742 (pt0) cc_final: 0.8479 (pm20) REVERT: B 31 LYS cc_start: 0.9450 (tttt) cc_final: 0.9137 (tttp) REVERT: B 53 GLU cc_start: 0.8581 (tp30) cc_final: 0.8180 (tm-30) REVERT: B 92 ARG cc_start: 0.9425 (ttp80) cc_final: 0.8901 (ttp80) REVERT: C 38 ASN cc_start: 0.8620 (p0) cc_final: 0.8273 (p0) REVERT: C 64 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9035 (pp20) REVERT: C 95 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9025 (tmmt) REVERT: D 42 TYR cc_start: 0.7958 (t80) cc_final: 0.7704 (t80) REVERT: D 47 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8931 (tm-30) REVERT: D 68 ASP cc_start: 0.9143 (t0) cc_final: 0.8761 (t0) REVERT: D 105 GLU cc_start: 0.8995 (tp30) cc_final: 0.8346 (tp30) REVERT: E 73 GLU cc_start: 0.8833 (tp30) cc_final: 0.8584 (tp30) REVERT: E 74 ILE cc_start: 0.9237 (tt) cc_final: 0.8926 (tt) REVERT: E 76 GLN cc_start: 0.9188 (pp30) cc_final: 0.8841 (pp30) REVERT: E 125 GLN cc_start: 0.8896 (mt0) cc_final: 0.8583 (mt0) REVERT: F 63 GLU cc_start: 0.9156 (tt0) cc_final: 0.8707 (mt-10) REVERT: F 88 TYR cc_start: 0.8503 (m-10) cc_final: 0.8266 (m-80) REVERT: G 24 GLN cc_start: 0.9352 (mm-40) cc_final: 0.8911 (mm110) REVERT: G 59 THR cc_start: 0.9301 (m) cc_final: 0.9000 (t) REVERT: G 90 ASP cc_start: 0.8087 (t0) cc_final: 0.7714 (t0) REVERT: G 100 VAL cc_start: 0.9659 (t) cc_final: 0.9381 (p) REVERT: G 101 THR cc_start: 0.9208 (m) cc_final: 0.8628 (p) REVERT: H 39 VAL cc_start: 0.9434 (m) cc_final: 0.9203 (p) REVERT: H 68 ASP cc_start: 0.9064 (t0) cc_final: 0.8767 (t0) REVERT: H 113 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 15 outliers final: 12 residues processed: 223 average time/residue: 0.1032 time to fit residues: 31.7666 Evaluate side-chains 227 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.043646 restraints weight = 46344.211| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.52 r_work: 0.2641 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12684 Z= 0.167 Angle : 0.677 8.675 18373 Z= 0.384 Chirality : 0.042 0.242 2090 Planarity : 0.004 0.044 1320 Dihedral : 31.333 175.302 3997 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.56 % Allowed : 33.87 % Favored : 63.58 % 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: 1.96 (0.31), residues: 734 helix: 1.97 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.66 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.040 0.002 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (12684) covalent geometry : angle 0.67715 / 0.38 (18373) hydrogen bonds : bond 0.04142 / 2.85 ( 767) hydrogen bonds : angle 3.09199 / 2.24 ( 1931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.80 seconds wall clock time: 36 minutes 3.22 seconds (2163.22 seconds total)