Starting phenix.real_space_refine on Fri Jul 3 01:59:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbx_36148/07_2026/8jbx_36148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbx_36148/07_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_36148/07_2026/8jbx_36148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbx_36148/07_2026/8jbx_36148_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jbx_36148/07_2026/8jbx_36148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbx_36148/07_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-dev-6108/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: 2.68, per 1000 atoms: 0.23 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: 1.30 Conformation dependent library (CDL) restraints added in 208.1 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: 1.97 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: 2.35 Time building geometry restraints manager: 1.65 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: 17383 1.64 - 3.29: 937 3.29 - 4.93: 41 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- 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= 0.515 Angle : 0.745 8.214 18373 Z= 0.650 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 0.74477 / 0.65 (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 : 0.320 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: 0.8905 (t0) REVERT: D 89 ILE cc_start: 0.9181 (mm) cc_final: 0.8864 (mm) REVERT: E 74 ILE cc_start: 0.9535 (tt) cc_final: 0.9303 (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: 0.8985 (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: 0.9108 (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: 0.1418 time to fit residues: 50.8042 Evaluate side-chains 222 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.058338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.043082 restraints weight = 46085.321| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.41 r_work: 0.2627 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12684 Z= 0.218 Angle : 0.682 9.662 18373 Z= 0.398 Chirality : 0.043 0.232 2090 Planarity : 0.005 0.056 1320 Dihedral : 31.014 175.053 3997 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.67 % Allowed : 27.96 % Favored : 68.37 % 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: 1.69 (0.31), residues: 734 helix: 1.92 (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 0.020 0.002 TYR C 39 PHE 0.014 0.001 PHE E 104 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (12684) covalent geometry : angle 0.68161 / 0.40 (18373) hydrogen bonds : bond 0.05024 / 3.47 ( 767) hydrogen bonds : angle 3.17236 / 2.27 ( 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 251 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 87 SER cc_start: 0.9399 (p) cc_final: 0.9156 (t) REVERT: A 94 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8597 (tp30) REVERT: A 108 ASN cc_start: 0.9399 (t0) cc_final: 0.9191 (t0) REVERT: B 27 GLN cc_start: 0.8648 (pt0) cc_final: 0.8385 (pm20) REVERT: B 31 LYS cc_start: 0.9418 (tttt) cc_final: 0.9047 (tttp) REVERT: B 53 GLU cc_start: 0.8750 (tp30) cc_final: 0.8051 (tp30) REVERT: B 84 MET cc_start: 0.8945 (tpp) cc_final: 0.8457 (tpt) REVERT: B 92 ARG cc_start: 0.9443 (ttp80) cc_final: 0.9022 (ttp80) REVERT: C 99 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8626 (tpp80) REVERT: D 42 TYR cc_start: 0.7863 (t80) cc_final: 0.7454 (t80) REVERT: D 47 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8835 (tm-30) REVERT: D 68 ASP cc_start: 0.9152 (t0) cc_final: 0.8796 (t0) REVERT: D 89 ILE cc_start: 0.8926 (mm) cc_final: 0.8704 (mm) REVERT: D 105 GLU cc_start: 0.9013 (tp30) cc_final: 0.8278 (tp30) REVERT: E 42 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.8009 (ttm110) REVERT: E 74 ILE cc_start: 0.9182 (tt) cc_final: 0.8929 (tt) REVERT: E 76 GLN cc_start: 0.9178 (pp30) cc_final: 0.8866 (pp30) REVERT: E 108 ASN cc_start: 0.9528 (t0) cc_final: 0.9218 (t0) REVERT: F 53 GLU cc_start: 0.9156 (tp30) cc_final: 0.8897 (tp30) REVERT: F 63 GLU cc_start: 0.9154 (tt0) cc_final: 0.8859 (mt-10) REVERT: F 85 ASP cc_start: 0.8951 (m-30) cc_final: 0.8733 (m-30) REVERT: G 59 THR cc_start: 0.9330 (m) cc_final: 0.9032 (t) REVERT: G 100 VAL cc_start: 0.9662 (t) cc_final: 0.9138 (p) REVERT: G 101 THR cc_start: 0.9076 (m) cc_final: 0.8575 (t) REVERT: H 33 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8018 (mmm-85) REVERT: H 105 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8612 (mm-30) REVERT: H 113 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8376 (tm-30) outliers start: 23 outliers final: 13 residues processed: 241 average time/residue: 0.1143 time to fit residues: 37.3249 Evaluate side-chains 227 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.058669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.043525 restraints weight = 46311.709| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.44 r_work: 0.2634 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12684 Z= 0.174 Angle : 0.643 8.272 18373 Z= 0.381 Chirality : 0.042 0.227 2090 Planarity : 0.004 0.049 1320 Dihedral : 31.104 175.655 3997 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 1.79 (0.31), residues: 734 helix: 2.01 (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 92 TYR 0.020 0.002 TYR C 39 PHE 0.007 0.001 PHE E 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (12684) covalent geometry : angle 0.64343 / 0.38 (18373) hydrogen bonds : bond 0.04604 / 3.20 ( 767) hydrogen bonds : angle 3.04401 / 2.19 ( 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 252 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.335 Fit side-chains REVERT: A 76 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8782 (tm-30) REVERT: A 87 SER cc_start: 0.9387 (p) cc_final: 0.9149 (t) REVERT: A 94 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8603 (tp30) REVERT: A 108 ASN cc_start: 0.9397 (t0) cc_final: 0.9174 (t0) REVERT: B 27 GLN cc_start: 0.8596 (pt0) cc_final: 0.8319 (pm20) REVERT: B 31 LYS cc_start: 0.9421 (tttt) cc_final: 0.9088 (tttp) REVERT: B 53 GLU cc_start: 0.8689 (tp30) cc_final: 0.7957 (tp30) REVERT: B 84 MET cc_start: 0.8947 (tpp) cc_final: 0.8536 (tpp) REVERT: B 92 ARG cc_start: 0.9482 (ttp80) cc_final: 0.9026 (ttp80) REVERT: C 99 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8683 (tpp80) REVERT: D 42 TYR cc_start: 0.7813 (t80) cc_final: 0.7428 (t80) REVERT: D 47 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8847 (tm-30) REVERT: D 57 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8259 (mmmm) REVERT: D 68 ASP cc_start: 0.9127 (t0) cc_final: 0.8755 (t0) REVERT: D 89 ILE cc_start: 0.8847 (mm) cc_final: 0.8575 (mm) REVERT: D 105 GLU cc_start: 0.8982 (tp30) cc_final: 0.8218 (tp30) REVERT: E 42 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: E 74 ILE cc_start: 0.9210 (tt) cc_final: 0.8943 (tt) REVERT: E 76 GLN cc_start: 0.9134 (pp30) cc_final: 0.8821 (pp30) REVERT: E 108 ASN cc_start: 0.9531 (t0) cc_final: 0.9205 (t0) REVERT: F 27 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.9069 (mp10) REVERT: F 53 GLU cc_start: 0.9169 (tp30) cc_final: 0.8939 (tp30) REVERT: F 63 GLU cc_start: 0.9142 (tt0) cc_final: 0.8832 (mt-10) REVERT: F 85 ASP cc_start: 0.9036 (m-30) cc_final: 0.8825 (m-30) REVERT: G 24 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8853 (mm-40) REVERT: G 59 THR cc_start: 0.9314 (m) cc_final: 0.9058 (t) REVERT: G 90 ASP cc_start: 0.8012 (t0) cc_final: 0.7679 (t0) REVERT: G 91 GLU cc_start: 0.8661 (tp30) cc_final: 0.8398 (tp30) REVERT: G 92 GLU cc_start: 0.9277 (mp0) cc_final: 0.8963 (tt0) REVERT: G 100 VAL cc_start: 0.9649 (t) cc_final: 0.9205 (p) REVERT: G 101 THR cc_start: 0.9068 (m) cc_final: 0.8535 (t) REVERT: H 33 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8077 (mmm-85) REVERT: H 62 MET cc_start: 0.9422 (tpp) cc_final: 0.9155 (mmm) REVERT: H 113 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8395 (tm-30) outliers start: 23 outliers final: 12 residues processed: 244 average time/residue: 0.1289 time to fit residues: 42.6594 Evaluate side-chains 228 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 27 GLN 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: 20.0000 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.0470 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 overall best weight: 0.9482 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.044515 restraints weight = 46248.528| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.47 r_work: 0.2656 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 0.047 12684 Z= 0.151 Angle : 0.614 7.020 18373 Z= 0.367 Chirality : 0.041 0.223 2090 Planarity : 0.004 0.051 1320 Dihedral : 31.163 175.689 3997 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.19 % Allowed : 28.27 % Favored : 68.53 % 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: 1.91 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.87 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 92 TYR 0.018 0.002 TYR D 40 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (12684) covalent geometry : angle 0.61400 / 0.37 (18373) hydrogen bonds : bond 0.04273 / 2.96 ( 767) hydrogen bonds : angle 2.98917 / 2.15 ( 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 254 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.375 Fit side-chains REVERT: A 76 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8772 (tm-30) REVERT: A 87 SER cc_start: 0.9363 (p) cc_final: 0.9123 (t) REVERT: A 94 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8609 (tp30) REVERT: B 27 GLN cc_start: 0.8609 (pt0) cc_final: 0.8330 (pm20) REVERT: B 31 LYS cc_start: 0.9452 (tttt) cc_final: 0.9121 (tttp) REVERT: B 84 MET cc_start: 0.8898 (tpp) cc_final: 0.8580 (tpp) REVERT: B 88 TYR cc_start: 0.8127 (t80) cc_final: 0.7808 (t80) REVERT: B 92 ARG cc_start: 0.9483 (ttp80) cc_final: 0.8989 (ttp80) REVERT: C 64 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.9008 (pp20) REVERT: C 84 GLN cc_start: 0.9419 (tp-100) cc_final: 0.9085 (tp-100) REVERT: D 42 TYR cc_start: 0.7805 (t80) cc_final: 0.7474 (t80) REVERT: D 47 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8870 (tm-30) REVERT: D 57 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8218 (mmmm) REVERT: D 68 ASP cc_start: 0.9145 (t0) cc_final: 0.8787 (t0) REVERT: D 89 ILE cc_start: 0.8795 (mm) cc_final: 0.8487 (mm) REVERT: D 105 GLU cc_start: 0.8929 (tp30) cc_final: 0.8362 (tp30) REVERT: E 42 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8112 (ttm-80) REVERT: E 74 ILE cc_start: 0.9206 (tt) cc_final: 0.8951 (tt) REVERT: E 76 GLN cc_start: 0.9156 (pp30) cc_final: 0.8808 (pp30) REVERT: E 108 ASN cc_start: 0.9470 (t0) cc_final: 0.9174 (t0) REVERT: F 63 GLU cc_start: 0.9134 (tt0) cc_final: 0.8842 (mt-10) REVERT: F 72 TYR cc_start: 0.8842 (m-80) cc_final: 0.8626 (m-80) REVERT: F 85 ASP cc_start: 0.9048 (m-30) cc_final: 0.8842 (m-30) REVERT: G 59 THR cc_start: 0.9298 (m) cc_final: 0.9048 (t) REVERT: G 91 GLU cc_start: 0.8676 (tp30) cc_final: 0.8363 (tp30) REVERT: G 92 GLU cc_start: 0.9318 (mp0) cc_final: 0.8935 (tt0) REVERT: G 100 VAL cc_start: 0.9628 (t) cc_final: 0.9173 (p) REVERT: G 101 THR cc_start: 0.9103 (m) cc_final: 0.8585 (t) REVERT: H 33 ARG cc_start: 0.8718 (ttm110) cc_final: 0.8087 (mmm-85) REVERT: H 35 GLU cc_start: 0.8073 (pt0) cc_final: 0.7819 (tt0) REVERT: H 62 MET cc_start: 0.9354 (tpp) cc_final: 0.9140 (mmm) REVERT: H 113 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8401 (tm-30) outliers start: 20 outliers final: 12 residues processed: 247 average time/residue: 0.1220 time to fit residues: 41.0910 Evaluate side-chains 231 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 40 SER Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.058843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.043876 restraints weight = 46421.993| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.46 r_work: 0.2639 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12684 Z= 0.165 Angle : 0.624 7.131 18373 Z= 0.368 Chirality : 0.041 0.223 2090 Planarity : 0.004 0.046 1320 Dihedral : 31.233 175.154 3997 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.04 % Allowed : 30.19 % Favored : 66.77 % 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: 1.90 (0.31), residues: 734 helix: 1.97 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.83 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 99 TYR 0.022 0.002 TYR D 40 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (12684) covalent geometry : angle 0.62393 / 0.37 (18373) hydrogen bonds : bond 0.04274 / 2.95 ( 767) hydrogen bonds : angle 2.98141 / 2.15 ( 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 244 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8955 (tp) REVERT: A 76 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 87 SER cc_start: 0.9353 (p) cc_final: 0.9119 (t) REVERT: A 94 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8537 (tp30) REVERT: B 27 GLN cc_start: 0.8627 (pt0) cc_final: 0.8358 (pm20) REVERT: B 31 LYS cc_start: 0.9466 (tttt) cc_final: 0.9128 (tttp) REVERT: B 53 GLU cc_start: 0.8508 (tp30) cc_final: 0.8001 (tp30) REVERT: B 84 MET cc_start: 0.8931 (tpp) cc_final: 0.8581 (tpp) REVERT: B 88 TYR cc_start: 0.8248 (t80) cc_final: 0.8018 (t80) REVERT: B 92 ARG cc_start: 0.9479 (ttp80) cc_final: 0.9001 (ttp80) REVERT: C 64 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9031 (pp20) REVERT: C 84 GLN cc_start: 0.9357 (tp-100) cc_final: 0.9051 (tp-100) REVERT: D 33 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.8008 (tpp-160) REVERT: D 42 TYR cc_start: 0.7858 (t80) cc_final: 0.7517 (t80) REVERT: D 47 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8906 (tm-30) REVERT: D 68 ASP cc_start: 0.9145 (t0) cc_final: 0.8792 (t0) REVERT: D 89 ILE cc_start: 0.8799 (mm) cc_final: 0.8444 (mm) REVERT: D 105 GLU cc_start: 0.8912 (tp30) cc_final: 0.8321 (tp30) REVERT: E 42 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8100 (ttm-80) REVERT: E 73 GLU cc_start: 0.8838 (tp30) cc_final: 0.8569 (tp30) REVERT: E 74 ILE cc_start: 0.9228 (tt) cc_final: 0.8956 (tt) REVERT: E 76 GLN cc_start: 0.9145 (pp30) cc_final: 0.8746 (pp30) REVERT: E 108 ASN cc_start: 0.9486 (t0) cc_final: 0.9195 (t0) REVERT: E 125 GLN cc_start: 0.8814 (mt0) cc_final: 0.8518 (mt0) REVERT: F 63 GLU cc_start: 0.9146 (tt0) cc_final: 0.8844 (mt-10) REVERT: F 85 ASP cc_start: 0.9067 (m-30) cc_final: 0.8848 (m-30) REVERT: G 24 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8821 (mm110) REVERT: G 59 THR cc_start: 0.9297 (m) cc_final: 0.9037 (t) REVERT: G 90 ASP cc_start: 0.7943 (t0) cc_final: 0.7573 (t0) REVERT: G 100 VAL cc_start: 0.9633 (t) cc_final: 0.9164 (p) REVERT: G 101 THR cc_start: 0.9134 (m) cc_final: 0.8615 (t) REVERT: H 33 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8097 (mmm-85) REVERT: H 62 MET cc_start: 0.9360 (tpp) cc_final: 0.9115 (mmm) REVERT: H 113 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8390 (tm-30) outliers start: 19 outliers final: 13 residues processed: 236 average time/residue: 0.1197 time to fit residues: 38.6500 Evaluate side-chains 230 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 B residue 66 ILE Chi-restraints excluded: chain B residue 71 THR 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 40 SER 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: 9.9990 chunk 28 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 E 55 GLN E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.040650 restraints weight = 47818.027| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.68 r_work: 0.2499 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12684 Z= 0.260 Angle : 0.700 7.404 18373 Z= 0.399 Chirality : 0.043 0.221 2090 Planarity : 0.004 0.047 1320 Dihedral : 31.476 174.553 3997 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.31 % Allowed : 30.35 % Favored : 65.34 % 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: 1.86 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 40 TYR 0.046 0.002 TYR D 40 PHE 0.007 0.001 PHE B 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 (12684) covalent geometry : angle 0.70022 / 0.40 (18373) hydrogen bonds : bond 0.05008 / 3.47 ( 767) hydrogen bonds : angle 3.19122 / 2.28 ( 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 239 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8645 (pm20) cc_final: 0.8379 (pm20) REVERT: A 76 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8752 (tm-30) REVERT: A 94 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8707 (tp30) REVERT: B 27 GLN cc_start: 0.8705 (pt0) cc_final: 0.8437 (pm20) REVERT: B 31 LYS cc_start: 0.9455 (tttt) cc_final: 0.9172 (tttp) REVERT: B 53 GLU cc_start: 0.8699 (tp30) cc_final: 0.8079 (tp30) REVERT: B 84 MET cc_start: 0.8939 (tpp) cc_final: 0.8611 (tpp) REVERT: B 92 ARG cc_start: 0.9460 (ttp80) cc_final: 0.9090 (ttp80) REVERT: C 38 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8445 (p0) REVERT: C 39 TYR cc_start: 0.8567 (m-10) cc_final: 0.8359 (m-10) REVERT: C 64 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.9055 (pp20) REVERT: D 42 TYR cc_start: 0.7964 (t80) cc_final: 0.7590 (t80) REVERT: D 47 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8926 (tm-30) REVERT: D 68 ASP cc_start: 0.9081 (t0) cc_final: 0.8727 (t0) REVERT: D 89 ILE cc_start: 0.8883 (mm) cc_final: 0.8529 (mm) REVERT: D 105 GLU cc_start: 0.8972 (tp30) cc_final: 0.8344 (tp30) REVERT: E 73 GLU cc_start: 0.8869 (tp30) cc_final: 0.8649 (tp30) REVERT: E 74 ILE cc_start: 0.9216 (tt) cc_final: 0.8910 (tt) REVERT: E 76 GLN cc_start: 0.9146 (pp30) cc_final: 0.8766 (pp30) REVERT: E 108 ASN cc_start: 0.9528 (t0) cc_final: 0.9281 (t0) REVERT: E 125 GLN cc_start: 0.8886 (mt0) cc_final: 0.8579 (mt0) REVERT: F 63 GLU cc_start: 0.9137 (tt0) cc_final: 0.8767 (mt-10) REVERT: F 85 ASP cc_start: 0.9089 (m-30) cc_final: 0.8820 (m-30) REVERT: G 24 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8973 (mm110) REVERT: G 59 THR cc_start: 0.9276 (m) cc_final: 0.9016 (t) REVERT: G 90 ASP cc_start: 0.8070 (t0) cc_final: 0.7744 (t0) REVERT: G 100 VAL cc_start: 0.9681 (t) cc_final: 0.9165 (p) REVERT: G 101 THR cc_start: 0.9128 (m) cc_final: 0.8645 (t) REVERT: H 33 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8074 (mmm-85) REVERT: H 113 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8423 (tm-30) outliers start: 27 outliers final: 18 residues processed: 230 average time/residue: 0.1167 time to fit residues: 36.9197 Evaluate side-chains 223 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 114 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 40 SER 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: 0.0870 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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** C 38 ASN D 63 ASN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043548 restraints weight = 46280.037| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.45 r_work: 0.2628 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12684 Z= 0.153 Angle : 0.630 6.686 18373 Z= 0.370 Chirality : 0.041 0.226 2090 Planarity : 0.004 0.044 1320 Dihedral : 31.399 175.638 3997 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.35 % Allowed : 31.31 % Favored : 65.34 % 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: 1.94 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.57 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 99 TYR 0.028 0.002 TYR B 88 PHE 0.008 0.001 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (12684) covalent geometry : angle 0.63032 / 0.37 (18373) hydrogen bonds : bond 0.04228 / 2.91 ( 767) hydrogen bonds : angle 3.00926 / 2.16 ( 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 250 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8281 (pm20) REVERT: A 76 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8750 (tm-30) REVERT: A 94 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8655 (tp30) REVERT: B 27 GLN cc_start: 0.8688 (pt0) cc_final: 0.8427 (pm20) REVERT: B 31 LYS cc_start: 0.9443 (tttt) cc_final: 0.9131 (tttp) REVERT: B 53 GLU cc_start: 0.8584 (tp30) cc_final: 0.8116 (tm-30) REVERT: B 84 MET cc_start: 0.8981 (tpp) cc_final: 0.8708 (tpp) REVERT: B 88 TYR cc_start: 0.8211 (t80) cc_final: 0.7934 (t80) REVERT: B 92 ARG cc_start: 0.9445 (ttp80) cc_final: 0.9081 (ttp80) REVERT: C 38 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8467 (p0) REVERT: C 39 TYR cc_start: 0.8666 (m-10) cc_final: 0.8460 (m-80) REVERT: C 64 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9030 (pp20) REVERT: C 84 GLN cc_start: 0.9393 (tp-100) cc_final: 0.9059 (tp-100) REVERT: D 42 TYR cc_start: 0.7911 (t80) cc_final: 0.7650 (t80) REVERT: D 47 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8921 (tm-30) REVERT: D 68 ASP cc_start: 0.9146 (t0) cc_final: 0.8758 (t0) REVERT: D 89 ILE cc_start: 0.8871 (mm) cc_final: 0.8528 (mm) REVERT: D 105 GLU cc_start: 0.8912 (tp30) cc_final: 0.8228 (tp30) REVERT: E 73 GLU cc_start: 0.8852 (tp30) cc_final: 0.8583 (tp30) REVERT: E 74 ILE cc_start: 0.9226 (tt) cc_final: 0.8921 (tt) REVERT: E 76 GLN cc_start: 0.9156 (pp30) cc_final: 0.8753 (pp30) REVERT: E 93 GLN cc_start: 0.9101 (tt0) cc_final: 0.8896 (tt0) REVERT: E 108 ASN cc_start: 0.9548 (t0) cc_final: 0.9281 (t0) REVERT: E 125 GLN cc_start: 0.8848 (mt0) cc_final: 0.8499 (mt0) REVERT: F 63 GLU cc_start: 0.9150 (tt0) cc_final: 0.8686 (mt-10) REVERT: F 74 GLU cc_start: 0.9468 (tp30) cc_final: 0.9172 (tp30) REVERT: F 84 MET cc_start: 0.8994 (mmm) cc_final: 0.8502 (mmm) REVERT: F 85 ASP cc_start: 0.9133 (m-30) cc_final: 0.8866 (m-30) REVERT: G 24 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8959 (mm110) REVERT: G 59 THR cc_start: 0.9301 (m) cc_final: 0.9013 (t) REVERT: G 75 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8527 (mmmm) REVERT: G 90 ASP cc_start: 0.8064 (t0) cc_final: 0.7578 (t0) REVERT: G 91 GLU cc_start: 0.8680 (tp30) cc_final: 0.8448 (tp30) REVERT: G 92 GLU cc_start: 0.9284 (mp0) cc_final: 0.8942 (tt0) REVERT: G 100 VAL cc_start: 0.9645 (t) cc_final: 0.9164 (p) REVERT: G 101 THR cc_start: 0.9204 (m) cc_final: 0.8716 (t) REVERT: H 33 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8062 (mmm-85) REVERT: H 113 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8404 (tm-30) outliers start: 21 outliers final: 16 residues processed: 242 average time/residue: 0.1099 time to fit residues: 36.8545 Evaluate side-chains 229 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 38 ASN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER 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 Chi-restraints excluded: chain H residue 98 VAL 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: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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** 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 = 0.3293 r_free = 0.3293 target = 0.059099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.043992 restraints weight = 45931.230| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.45 r_work: 0.2636 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12684 Z= 0.152 Angle : 0.638 8.037 18373 Z= 0.370 Chirality : 0.041 0.264 2090 Planarity : 0.004 0.044 1320 Dihedral : 31.353 175.393 3997 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 33.23 % Favored : 64.06 % 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: 1.94 (0.31), residues: 734 helix: 1.94 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.59 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.024 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (12684) covalent geometry : angle 0.63843 / 0.37 (18373) hydrogen bonds : bond 0.04118 / 2.83 ( 767) hydrogen bonds : angle 3.00503 / 2.17 ( 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 239 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8549 (pm20) cc_final: 0.8272 (pm20) REVERT: A 60 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9093 (tp) REVERT: A 76 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 94 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8605 (tp30) REVERT: B 27 GLN cc_start: 0.8697 (pt0) cc_final: 0.8379 (pm20) REVERT: B 31 LYS cc_start: 0.9445 (tttt) cc_final: 0.9134 (tttp) REVERT: B 53 GLU cc_start: 0.8560 (tp30) cc_final: 0.8145 (tm-30) REVERT: B 84 MET cc_start: 0.8980 (tpp) cc_final: 0.8685 (tpp) REVERT: B 88 TYR cc_start: 0.8285 (t80) cc_final: 0.7907 (t80) REVERT: B 92 ARG cc_start: 0.9451 (ttp80) cc_final: 0.9091 (ttp80) REVERT: C 64 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.9035 (pp20) REVERT: C 84 GLN cc_start: 0.9379 (tp-100) cc_final: 0.9123 (tp-100) REVERT: C 95 LYS cc_start: 0.9375 (ttmt) cc_final: 0.9028 (tmmt) REVERT: D 42 TYR cc_start: 0.7903 (t80) cc_final: 0.7645 (t80) REVERT: D 47 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8906 (tm-30) REVERT: D 68 ASP cc_start: 0.9147 (t0) cc_final: 0.8775 (t0) REVERT: D 89 ILE cc_start: 0.8840 (mm) cc_final: 0.8455 (mm) REVERT: D 105 GLU cc_start: 0.8891 (tp30) cc_final: 0.8210 (tp30) REVERT: E 73 GLU cc_start: 0.8873 (tp30) cc_final: 0.8595 (tp30) REVERT: E 74 ILE cc_start: 0.9244 (tt) cc_final: 0.8929 (tt) REVERT: E 76 GLN cc_start: 0.9142 (pp30) cc_final: 0.8740 (pp30) REVERT: E 108 ASN cc_start: 0.9532 (t0) cc_final: 0.9253 (t0) REVERT: E 125 GLN cc_start: 0.8832 (mt0) cc_final: 0.8473 (mt0) REVERT: F 63 GLU cc_start: 0.9148 (tt0) cc_final: 0.8690 (mt-10) REVERT: F 84 MET cc_start: 0.9011 (mmm) cc_final: 0.8506 (mmm) REVERT: F 85 ASP cc_start: 0.9134 (m-30) cc_final: 0.8882 (m-30) REVERT: G 24 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8851 (mm110) REVERT: G 35 ARG cc_start: 0.9448 (mtm110) cc_final: 0.8794 (mtm-85) REVERT: G 59 THR cc_start: 0.9279 (m) cc_final: 0.8974 (t) REVERT: G 75 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8552 (mmmm) REVERT: G 90 ASP cc_start: 0.8035 (t0) cc_final: 0.7540 (t0) REVERT: G 91 GLU cc_start: 0.8664 (tp30) cc_final: 0.8410 (tp30) REVERT: G 92 GLU cc_start: 0.9308 (mp0) cc_final: 0.8922 (tt0) REVERT: G 100 VAL cc_start: 0.9640 (t) cc_final: 0.9159 (p) REVERT: G 101 THR cc_start: 0.9206 (m) cc_final: 0.8711 (t) REVERT: H 113 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8436 (tm-30) outliers start: 17 outliers final: 13 residues processed: 233 average time/residue: 0.1128 time to fit residues: 35.9789 Evaluate side-chains 230 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 C residue 114 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 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: 0.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** ** C 38 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 = 0.3269 r_free = 0.3269 target = 0.058379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043473 restraints weight = 46465.474| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.49 r_work: 0.2631 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2093 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= 0.160 Angle : 0.644 8.168 18373 Z= 0.373 Chirality : 0.041 0.222 2090 Planarity : 0.004 0.043 1320 Dihedral : 31.358 175.100 3997 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.04 % Allowed : 33.07 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.31), residues: 734 helix: 1.91 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.63 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.032 0.002 TYR H 40 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (12684) covalent geometry : angle 0.64446 / 0.37 (18373) hydrogen bonds : bond 0.04120 / 2.83 ( 767) hydrogen bonds : angle 3.02015 / 2.17 ( 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 239 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8486 (pm20) cc_final: 0.8217 (pm20) REVERT: A 60 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8971 (tp) REVERT: A 76 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 94 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 27 GLN cc_start: 0.8718 (pt0) cc_final: 0.8390 (pm20) REVERT: B 31 LYS cc_start: 0.9446 (tttt) cc_final: 0.9132 (tttp) REVERT: B 53 GLU cc_start: 0.8559 (tp30) cc_final: 0.8152 (tm-30) REVERT: B 84 MET cc_start: 0.9007 (tpp) cc_final: 0.8706 (tpp) REVERT: B 88 TYR cc_start: 0.8271 (t80) cc_final: 0.7960 (t80) REVERT: B 92 ARG cc_start: 0.9442 (ttp80) cc_final: 0.9082 (ttp80) REVERT: C 64 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.9006 (pp20) REVERT: C 84 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9110 (tp-100) REVERT: C 95 LYS cc_start: 0.9369 (ttmt) cc_final: 0.9044 (tmmt) REVERT: D 33 ARG cc_start: 0.8295 (tpp-160) cc_final: 0.8052 (tpp-160) REVERT: D 42 TYR cc_start: 0.7916 (t80) cc_final: 0.7679 (t80) REVERT: D 47 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8921 (tm-30) REVERT: D 68 ASP cc_start: 0.9153 (t0) cc_final: 0.8777 (t0) REVERT: D 80 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9015 (mp) REVERT: D 89 ILE cc_start: 0.8834 (mm) cc_final: 0.8627 (mm) REVERT: D 105 GLU cc_start: 0.8936 (tp30) cc_final: 0.8277 (tp30) REVERT: E 73 GLU cc_start: 0.8874 (tp30) cc_final: 0.8589 (tp30) REVERT: E 74 ILE cc_start: 0.9251 (tt) cc_final: 0.8929 (tt) REVERT: E 76 GLN cc_start: 0.9144 (pp30) cc_final: 0.8772 (pp30) REVERT: E 108 ASN cc_start: 0.9518 (t0) cc_final: 0.9245 (t0) REVERT: F 63 GLU cc_start: 0.9155 (tt0) cc_final: 0.8706 (mt-10) REVERT: F 85 ASP cc_start: 0.9119 (m-30) cc_final: 0.8872 (m-30) REVERT: G 24 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8902 (mm110) REVERT: G 35 ARG cc_start: 0.9448 (mtm110) cc_final: 0.8790 (mtm-85) REVERT: G 59 THR cc_start: 0.9299 (m) cc_final: 0.9000 (t) REVERT: G 75 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8586 (mmmm) REVERT: G 90 ASP cc_start: 0.8024 (t0) cc_final: 0.7525 (t0) REVERT: G 91 GLU cc_start: 0.8699 (tp30) cc_final: 0.8447 (tp30) REVERT: G 92 GLU cc_start: 0.9323 (mp0) cc_final: 0.8951 (tt0) REVERT: G 100 VAL cc_start: 0.9641 (t) cc_final: 0.9156 (p) REVERT: G 101 THR cc_start: 0.9213 (m) cc_final: 0.8752 (t) REVERT: H 113 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8464 (tm-30) outliers start: 19 outliers final: 14 residues processed: 232 average time/residue: 0.1070 time to fit residues: 34.1005 Evaluate side-chains 229 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 C residue 114 VAL Chi-restraints excluded: chain D residue 80 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.059008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.044131 restraints weight = 46494.815| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.49 r_work: 0.2658 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12684 Z= 0.150 Angle : 0.640 8.308 18373 Z= 0.371 Chirality : 0.041 0.220 2090 Planarity : 0.004 0.053 1320 Dihedral : 31.331 175.342 3997 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.56 % Allowed : 33.71 % Favored : 63.74 % 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: 1.97 (0.31), residues: 734 helix: 1.99 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.67 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.030 0.002 TYR H 40 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12684) covalent geometry : angle 0.63986 / 0.37 (18373) hydrogen bonds : bond 0.04011 / 2.75 ( 767) hydrogen bonds : angle 3.00965 / 2.17 ( 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 243 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8436 (pm20) cc_final: 0.8171 (pm20) REVERT: A 60 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8919 (tp) REVERT: A 94 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8676 (tp30) REVERT: B 27 GLN cc_start: 0.8723 (pt0) cc_final: 0.8404 (pm20) REVERT: B 31 LYS cc_start: 0.9449 (tttt) cc_final: 0.9132 (tttp) REVERT: B 53 GLU cc_start: 0.8484 (tp30) cc_final: 0.8115 (tm-30) REVERT: B 88 TYR cc_start: 0.8239 (t80) cc_final: 0.7856 (t80) REVERT: B 92 ARG cc_start: 0.9428 (ttp80) cc_final: 0.9080 (ttp80) REVERT: C 36 LYS cc_start: 0.9286 (tppt) cc_final: 0.8908 (tppt) REVERT: C 64 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9002 (pp20) REVERT: C 84 GLN cc_start: 0.9313 (tp-100) cc_final: 0.9095 (tp-100) REVERT: C 95 LYS cc_start: 0.9349 (ttmt) cc_final: 0.9025 (tmmt) REVERT: D 33 ARG cc_start: 0.8305 (tpp-160) cc_final: 0.8084 (tpp-160) REVERT: D 42 TYR cc_start: 0.7905 (t80) cc_final: 0.7652 (t80) REVERT: D 47 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8954 (tm-30) REVERT: D 68 ASP cc_start: 0.9149 (t0) cc_final: 0.8772 (t0) REVERT: D 105 GLU cc_start: 0.8926 (tp30) cc_final: 0.8285 (tp30) REVERT: E 73 GLU cc_start: 0.8855 (tp30) cc_final: 0.8584 (tp30) REVERT: E 74 ILE cc_start: 0.9231 (tt) cc_final: 0.8909 (tt) REVERT: E 76 GLN cc_start: 0.9148 (pp30) cc_final: 0.8786 (pp30) REVERT: E 108 ASN cc_start: 0.9497 (t0) cc_final: 0.9219 (t0) REVERT: F 63 GLU cc_start: 0.9136 (tt0) cc_final: 0.8682 (mt-10) REVERT: F 77 LYS cc_start: 0.9656 (mttp) cc_final: 0.9245 (mmtm) REVERT: F 84 MET cc_start: 0.8928 (mmm) cc_final: 0.8652 (mmm) REVERT: F 85 ASP cc_start: 0.9058 (m-30) cc_final: 0.8839 (m-30) REVERT: G 24 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8934 (mm110) REVERT: G 35 ARG cc_start: 0.9445 (mtm110) cc_final: 0.8818 (mtm-85) REVERT: G 56 GLU cc_start: 0.8859 (tt0) cc_final: 0.8229 (tt0) REVERT: G 59 THR cc_start: 0.9271 (m) cc_final: 0.8972 (t) REVERT: G 75 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8632 (mmmm) REVERT: G 90 ASP cc_start: 0.7961 (t0) cc_final: 0.7464 (t0) REVERT: G 91 GLU cc_start: 0.8688 (tp30) cc_final: 0.8430 (tp30) REVERT: G 92 GLU cc_start: 0.9331 (mp0) cc_final: 0.8914 (tt0) REVERT: G 100 VAL cc_start: 0.9635 (t) cc_final: 0.9149 (p) REVERT: G 101 THR cc_start: 0.9227 (m) cc_final: 0.8727 (t) REVERT: H 62 MET cc_start: 0.9382 (mmm) cc_final: 0.9004 (mmm) REVERT: H 71 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9204 (tp30) REVERT: H 113 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 16 outliers final: 11 residues processed: 236 average time/residue: 0.1219 time to fit residues: 39.3934 Evaluate side-chains 231 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 C residue 114 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044557 restraints weight = 46122.732| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.49 r_work: 0.2667 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 12684 Z= 0.152 Angle : 0.647 8.406 18373 Z= 0.373 Chirality : 0.040 0.220 2090 Planarity : 0.004 0.057 1320 Dihedral : 31.340 175.094 3997 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.56 % Allowed : 33.55 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.31), residues: 734 helix: 1.98 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.73 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 92 TYR 0.033 0.002 TYR D 40 PHE 0.012 0.001 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (12684) covalent geometry : angle 0.64725 / 0.37 (18373) hydrogen bonds : bond 0.04012 / 2.75 ( 767) hydrogen bonds : angle 3.07755 / 2.23 ( 1931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.03 seconds wall clock time: 41 minutes 19.44 seconds (2479.44 seconds total)