Starting phenix.real_space_refine on Tue Jul 29 16:58:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbx_36148/07_2025/8jbx_36148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbx_36148/07_2025/8jbx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jbx_36148/07_2025/8jbx_36148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbx_36148/07_2025/8jbx_36148.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbx_36148/07_2025/8jbx_36148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbx_36148/07_2025/8jbx_36148_neut.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.17, per 1000 atoms: 0.60 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: 2.66 Conformation dependent library (CDL) restraints added in 853.5 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: 5.32 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: 4.36 Time building geometry restraints manager: 3.23 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 1.460 1.388 0.072 2.00e-02 2.50e+03 1.30e+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=" CA SER E 57 " pdb=" C SER E 57 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.35e-02 5.49e+03 6.57e+00 bond pdb=" CA ASP F 85 " pdb=" CB ASP F 85 " ideal model delta sigma weight residual 1.529 1.493 0.036 1.58e-02 4.01e+03 5.06e+00 bond pdb=" C ASP F 85 " pdb=" N VAL F 86 " ideal model delta sigma weight residual 1.335 1.312 0.023 1.26e-02 6.30e+03 3.36e+00 ... (remaining 12679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 17871 1.64 - 3.29: 459 3.29 - 4.93: 32 4.93 - 6.57: 8 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=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.67e+00 angle pdb=" CB MET F 84 " pdb=" CG MET F 84 " pdb=" SD MET F 84 " ideal model delta sigma weight residual 112.70 120.91 -8.21 3.00e+00 1.11e-01 7.50e+00 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" CB MET E 90 " pdb=" CG MET E 90 " pdb=" SD MET E 90 " ideal model delta sigma weight residual 112.70 120.33 -7.63 3.00e+00 1.11e-01 6.47e+00 ... (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: 1540 0.033 - 0.066: 443 0.066 - 0.099: 72 0.099 - 0.132: 30 0.132 - 0.164: 5 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=" 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 chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2087 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 84 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C MET F 84 " -0.054 2.00e-02 2.50e+03 pdb=" O MET F 84 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP F 85 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 49 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO D 50 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.001 2.00e-02 2.50e+03 1.28e-02 3.28e+00 pdb=" CG TYR F 88 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " -0.014 2.00e-02 2.50e+03 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2028 2.77 - 3.31: 10993 3.31 - 3.84: 24017 3.84 - 4.37: 26289 4.37 - 4.90: 38419 Nonbonded interactions: 101746 Sorted by model distance: nonbonded pdb=" NH1 ARG C 81 " pdb=" O GLY C 106 " model vdw 2.242 3.120 nonbonded pdb=" NH2 ARG F 92 " pdb=" OE1 GLU H 76 " model vdw 2.245 3.120 nonbonded pdb=" O SER D 124 " pdb=" OG SER D 124 " model vdw 2.249 3.040 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DT I -42 " model vdw 2.266 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE2 GLU E 133 " model vdw 2.279 3.040 ... (remaining 101741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.800 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 0.004 0.072 12684 Z= 0.181 Angle : 0.584 8.214 18373 Z= 0.347 Chirality : 0.033 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.009 0.001 HIS D 82 PHE 0.007 0.001 PHE E 78 TYR 0.024 0.002 TYR D 121 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.09436 ( 767) hydrogen bonds : angle 3.58959 ( 1931) covalent geometry : bond 0.00387 (12684) covalent geometry : angle 0.58389 (18373) *********************** 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 : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8619 (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: 0.8830 (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: 0.8756 (mtm-85) REVERT: G 59 THR cc_start: 0.9519 (m) cc_final: 0.9303 (t) REVERT: G 71 ARG cc_start: 0.9184 (ttp-110) cc_final: 0.8769 (ttp-110) REVERT: G 100 VAL cc_start: 0.9353 (t) cc_final: 0.9109 (p) REVERT: G 101 THR cc_start: 0.9279 (m) cc_final: 0.8910 (t) REVERT: H 45 LEU cc_start: 0.9633 (tp) cc_final: 0.9383 (tt) REVERT: H 113 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8180 (tm-30) outliers start: 3 outliers final: 0 residues processed: 270 average time/residue: 0.3065 time to fit residues: 108.1512 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 : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 63 ASN E 55 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.057517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.042179 restraints weight = 46095.688| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.44 r_work: 0.2605 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12684 Z= 0.241 Angle : 0.620 7.909 18373 Z= 0.360 Chirality : 0.036 0.169 2090 Planarity : 0.004 0.055 1320 Dihedral : 30.837 177.943 3997 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.47 % Allowed : 27.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.31), residues: 734 helix: 2.01 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.08 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE B 100 TYR 0.013 0.002 TYR C 39 ARG 0.005 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 767) hydrogen bonds : angle 3.04888 ( 1931) covalent geometry : bond 0.00541 (12684) covalent geometry : angle 0.62015 (18373) *********************** 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 260 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8411 (pm20) cc_final: 0.8183 (pm20) REVERT: A 76 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8790 (tm-30) REVERT: A 87 SER cc_start: 0.9418 (p) cc_final: 0.9211 (t) REVERT: A 94 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8668 (tp30) REVERT: B 27 GLN cc_start: 0.8640 (pt0) cc_final: 0.8351 (pm20) REVERT: B 31 LYS cc_start: 0.9441 (tttt) cc_final: 0.9123 (tttp) REVERT: B 53 GLU cc_start: 0.8804 (tp30) cc_final: 0.8078 (tp30) REVERT: B 84 MET cc_start: 0.8997 (tpp) cc_final: 0.8430 (tpt) REVERT: B 92 ARG cc_start: 0.9430 (ttp80) cc_final: 0.9013 (ttp80) REVERT: C 99 ARG cc_start: 0.8904 (tpp80) cc_final: 0.8702 (tpp80) REVERT: D 42 TYR cc_start: 0.7889 (t80) cc_final: 0.7507 (t80) REVERT: D 47 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8880 (tm-30) REVERT: D 68 ASP cc_start: 0.9122 (t0) cc_final: 0.8763 (t0) REVERT: D 79 ARG cc_start: 0.9362 (mtm180) cc_final: 0.9158 (ttp-110) REVERT: D 89 ILE cc_start: 0.8973 (mm) cc_final: 0.8668 (mm) REVERT: D 105 GLU cc_start: 0.8943 (tp30) cc_final: 0.8152 (tp30) REVERT: E 42 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7935 (ttm110) REVERT: E 74 ILE cc_start: 0.9161 (tt) cc_final: 0.8938 (tt) REVERT: E 76 GLN cc_start: 0.9197 (pp30) cc_final: 0.8867 (pp30) REVERT: E 108 ASN cc_start: 0.9517 (t0) cc_final: 0.9243 (t0) REVERT: F 63 GLU cc_start: 0.9166 (tt0) cc_final: 0.8820 (mt-10) REVERT: G 35 ARG cc_start: 0.9436 (mtm110) cc_final: 0.8789 (mtm-85) REVERT: G 59 THR cc_start: 0.9299 (m) cc_final: 0.9023 (t) REVERT: G 73 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.8971 (t0) REVERT: G 100 VAL cc_start: 0.9667 (t) cc_final: 0.9146 (p) REVERT: G 101 THR cc_start: 0.9093 (m) cc_final: 0.8590 (t) REVERT: H 40 TYR cc_start: 0.9198 (m-80) cc_final: 0.8947 (m-80) REVERT: H 105 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8064 (mm-30) REVERT: H 113 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8388 (tm-30) outliers start: 28 outliers final: 16 residues processed: 247 average time/residue: 0.2978 time to fit residues: 97.8436 Evaluate side-chains 233 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 B residue 81 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 73 ASN 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 34 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** 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 = 0.3189 r_free = 0.3189 target = 0.055793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.040605 restraints weight = 47815.262| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.71 r_work: 0.2521 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12684 Z= 0.251 Angle : 0.629 7.011 18373 Z= 0.365 Chirality : 0.036 0.167 2090 Planarity : 0.004 0.040 1320 Dihedral : 30.986 177.330 3997 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.43 % Allowed : 28.27 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.31), residues: 734 helix: 2.00 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE B 100 TYR 0.042 0.002 TYR D 40 ARG 0.007 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 767) hydrogen bonds : angle 3.07654 ( 1931) covalent geometry : bond 0.00568 (12684) covalent geometry : angle 0.62884 (18373) *********************** 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 256 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8663 (pm20) cc_final: 0.8333 (pm20) REVERT: A 68 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8890 (tp40) REVERT: A 76 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 94 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8750 (tp30) REVERT: B 27 GLN cc_start: 0.8725 (pt0) cc_final: 0.8440 (pm20) REVERT: B 31 LYS cc_start: 0.9470 (tttt) cc_final: 0.9197 (tttp) REVERT: B 53 GLU cc_start: 0.8884 (tp30) cc_final: 0.8190 (tp30) REVERT: B 84 MET cc_start: 0.8916 (tpp) cc_final: 0.8451 (tpt) REVERT: B 92 ARG cc_start: 0.9446 (ttp80) cc_final: 0.8968 (ttp80) REVERT: C 64 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9048 (pp20) REVERT: D 42 TYR cc_start: 0.7966 (t80) cc_final: 0.7568 (t80) REVERT: D 47 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8947 (tm-30) REVERT: D 68 ASP cc_start: 0.9149 (t0) cc_final: 0.8801 (t0) REVERT: D 105 GLU cc_start: 0.8981 (tp30) cc_final: 0.8438 (tp30) REVERT: E 72 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7936 (mtt90) REVERT: E 74 ILE cc_start: 0.9182 (tt) cc_final: 0.8919 (tt) REVERT: E 76 GLN cc_start: 0.9188 (pp30) cc_final: 0.8828 (pp30) REVERT: F 53 GLU cc_start: 0.9256 (tp30) cc_final: 0.8992 (tp30) REVERT: F 63 GLU cc_start: 0.9166 (tt0) cc_final: 0.8764 (mt-10) REVERT: F 84 MET cc_start: 0.8853 (mmm) cc_final: 0.8573 (tmm) REVERT: F 85 ASP cc_start: 0.8974 (m-30) cc_final: 0.8594 (m-30) REVERT: G 59 THR cc_start: 0.9294 (m) cc_final: 0.8948 (t) REVERT: G 73 ASN cc_start: 0.9358 (OUTLIER) cc_final: 0.9144 (t0) REVERT: G 75 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8685 (mmmm) REVERT: G 90 ASP cc_start: 0.8102 (t0) cc_final: 0.7877 (t0) REVERT: G 91 GLU cc_start: 0.8872 (tp30) cc_final: 0.8627 (tp30) REVERT: G 92 GLU cc_start: 0.9381 (mp0) cc_final: 0.9022 (tt0) REVERT: G 100 VAL cc_start: 0.9682 (t) cc_final: 0.9195 (p) REVERT: G 101 THR cc_start: 0.9238 (m) cc_final: 0.8759 (t) REVERT: H 68 ASP cc_start: 0.9090 (t0) cc_final: 0.8886 (t0) REVERT: H 113 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8458 (tm-30) outliers start: 34 outliers final: 19 residues processed: 245 average time/residue: 0.2903 time to fit residues: 94.8035 Evaluate side-chains 234 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 68 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 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 C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 72 ARG 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 F residue 86 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 73 ASN 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 88 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.039082 restraints weight = 47895.440| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.64 r_work: 0.2482 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 12684 Z= 0.314 Angle : 0.666 7.862 18373 Z= 0.385 Chirality : 0.038 0.162 2090 Planarity : 0.004 0.046 1320 Dihedral : 31.168 177.329 3997 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 7.67 % Allowed : 26.36 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.31), residues: 734 helix: 1.95 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.95 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE B 100 TYR 0.050 0.003 TYR D 40 ARG 0.009 0.001 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 767) hydrogen bonds : angle 3.24000 ( 1931) covalent geometry : bond 0.00713 (12684) covalent geometry : angle 0.66583 (18373) *********************** 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 261 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8765 (pm20) cc_final: 0.8403 (pm20) REVERT: A 68 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8922 (tp40) REVERT: A 76 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8759 (tm-30) REVERT: A 94 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8816 (tp30) REVERT: A 133 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: B 27 GLN cc_start: 0.8745 (pt0) cc_final: 0.8430 (pm20) REVERT: B 31 LYS cc_start: 0.9479 (tttt) cc_final: 0.9205 (tttp) REVERT: B 53 GLU cc_start: 0.9021 (tp30) cc_final: 0.8250 (tp30) REVERT: B 84 MET cc_start: 0.8906 (tpp) cc_final: 0.8096 (tpp) REVERT: B 88 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: B 92 ARG cc_start: 0.9403 (ttp80) cc_final: 0.9049 (ttp80) REVERT: C 61 GLU cc_start: 0.9052 (tp30) cc_final: 0.8699 (tp30) REVERT: C 64 GLU cc_start: 0.9391 (pp20) cc_final: 0.9074 (pp20) REVERT: C 84 GLN cc_start: 0.9557 (tp-100) cc_final: 0.9330 (tp-100) REVERT: D 42 TYR cc_start: 0.7984 (t80) cc_final: 0.7620 (t80) REVERT: D 47 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8892 (tm-30) REVERT: D 68 ASP cc_start: 0.9149 (t0) cc_final: 0.8780 (t0) REVERT: D 105 GLU cc_start: 0.8992 (tp30) cc_final: 0.8590 (tp30) REVERT: E 72 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7863 (mtt90) REVERT: E 76 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8830 (pp30) REVERT: F 53 GLU cc_start: 0.9271 (tp30) cc_final: 0.9024 (tp30) REVERT: F 74 GLU cc_start: 0.9453 (tp30) cc_final: 0.9146 (tp30) REVERT: F 84 MET cc_start: 0.9017 (mmm) cc_final: 0.8546 (tmm) REVERT: F 85 ASP cc_start: 0.9023 (m-30) cc_final: 0.8599 (m-30) REVERT: G 73 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.9125 (t0) REVERT: G 75 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8730 (mmmm) REVERT: G 100 VAL cc_start: 0.9723 (t) cc_final: 0.9250 (p) REVERT: G 101 THR cc_start: 0.9306 (m) cc_final: 0.8834 (t) REVERT: H 68 ASP cc_start: 0.9127 (t0) cc_final: 0.8879 (t0) REVERT: H 113 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8468 (tm-30) outliers start: 48 outliers final: 32 residues processed: 241 average time/residue: 0.2727 time to fit residues: 88.3297 Evaluate side-chains 245 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 68 GLN Chi-restraints excluded: chain A residue 74 ILE 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 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 100 LEU 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 F residue 86 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 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 = 0.3247 r_free = 0.3247 target = 0.057330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.042449 restraints weight = 46146.746| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.48 r_work: 0.2607 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12684 Z= 0.165 Angle : 0.598 6.645 18373 Z= 0.350 Chirality : 0.034 0.167 2090 Planarity : 0.004 0.042 1320 Dihedral : 30.971 177.952 3997 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.79 % Allowed : 30.83 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.31), residues: 734 helix: 1.99 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.82 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.038 0.002 TYR D 40 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 767) hydrogen bonds : angle 2.92890 ( 1931) covalent geometry : bond 0.00365 (12684) covalent geometry : angle 0.59824 (18373) *********************** 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 264 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8649 (pm20) cc_final: 0.8284 (pm20) REVERT: A 76 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 94 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8666 (tp30) REVERT: B 27 GLN cc_start: 0.8755 (pt0) cc_final: 0.8420 (pm20) REVERT: B 31 LYS cc_start: 0.9452 (tttt) cc_final: 0.9152 (tttp) REVERT: B 53 GLU cc_start: 0.8819 (tp30) cc_final: 0.8159 (tp30) REVERT: B 84 MET cc_start: 0.8868 (tpp) cc_final: 0.8204 (tpp) REVERT: B 88 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: B 92 ARG cc_start: 0.9337 (ttp80) cc_final: 0.8873 (ttp80) REVERT: C 38 ASN cc_start: 0.8674 (p0) cc_final: 0.8354 (p0) REVERT: C 61 GLU cc_start: 0.8977 (tp30) cc_final: 0.8545 (tp30) REVERT: C 64 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9033 (pp20) REVERT: D 42 TYR cc_start: 0.7898 (t80) cc_final: 0.7610 (t80) REVERT: D 47 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8890 (tm-30) REVERT: D 57 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8366 (mmmm) REVERT: D 68 ASP cc_start: 0.9118 (t0) cc_final: 0.8746 (t0) REVERT: D 80 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9035 (mp) REVERT: D 83 TYR cc_start: 0.8489 (t80) cc_final: 0.8122 (t80) REVERT: D 105 GLU cc_start: 0.8925 (tp30) cc_final: 0.8374 (tp30) REVERT: E 72 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7991 (mtt-85) REVERT: E 76 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8855 (pp30) REVERT: F 53 GLU cc_start: 0.9224 (tp30) cc_final: 0.8943 (tp30) REVERT: F 63 GLU cc_start: 0.9158 (tt0) cc_final: 0.8757 (mt-10) REVERT: F 84 MET cc_start: 0.8913 (mmm) cc_final: 0.8400 (tmm) REVERT: F 85 ASP cc_start: 0.8919 (m-30) cc_final: 0.8482 (m-30) REVERT: G 35 ARG cc_start: 0.9429 (mtm110) cc_final: 0.8766 (mtm-85) REVERT: G 59 THR cc_start: 0.9274 (m) cc_final: 0.8971 (t) REVERT: G 73 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9053 (t0) REVERT: G 75 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8179 (mmmm) REVERT: G 90 ASP cc_start: 0.7981 (t0) cc_final: 0.7747 (t0) REVERT: G 91 GLU cc_start: 0.8755 (tp30) cc_final: 0.8469 (tp30) REVERT: G 92 GLU cc_start: 0.9372 (mp0) cc_final: 0.9071 (mt-10) REVERT: G 100 VAL cc_start: 0.9684 (t) cc_final: 0.9165 (p) REVERT: G 101 THR cc_start: 0.9250 (m) cc_final: 0.8781 (t) REVERT: H 62 MET cc_start: 0.9377 (tpp) cc_final: 0.9152 (mmm) REVERT: H 68 ASP cc_start: 0.9162 (t0) cc_final: 0.8866 (t0) REVERT: H 113 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8503 (tm-30) outliers start: 30 outliers final: 17 residues processed: 251 average time/residue: 0.2893 time to fit residues: 96.9632 Evaluate side-chains 244 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 118 THR 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 B residue 88 TYR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 73 ASN 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: 7.9990 chunk 83 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN ** E 108 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 = 0.3236 r_free = 0.3236 target = 0.056712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.041809 restraints weight = 47224.367| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.49 r_work: 0.2588 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12684 Z= 0.207 Angle : 0.608 6.724 18373 Z= 0.355 Chirality : 0.034 0.162 2090 Planarity : 0.004 0.044 1320 Dihedral : 30.988 177.672 3997 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.95 % Allowed : 30.03 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.31), residues: 734 helix: 2.03 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.73 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE B 100 TYR 0.015 0.002 TYR H 40 ARG 0.006 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 767) hydrogen bonds : angle 2.98811 ( 1931) covalent geometry : bond 0.00467 (12684) covalent geometry : angle 0.60829 (18373) *********************** 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 249 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.8271 (pm20) REVERT: A 68 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8900 (tt0) REVERT: A 76 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 94 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8689 (tp30) REVERT: B 27 GLN cc_start: 0.8742 (pt0) cc_final: 0.8382 (pm20) REVERT: B 53 GLU cc_start: 0.8886 (tp30) cc_final: 0.8211 (tp30) REVERT: B 84 MET cc_start: 0.8878 (tpp) cc_final: 0.8171 (tpp) REVERT: B 88 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: B 92 ARG cc_start: 0.9357 (ttp80) cc_final: 0.8878 (ttp80) REVERT: C 38 ASN cc_start: 0.8748 (p0) cc_final: 0.8449 (p0) REVERT: C 61 GLU cc_start: 0.8991 (tp30) cc_final: 0.8559 (tp30) REVERT: C 64 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9045 (pp20) REVERT: C 84 GLN cc_start: 0.9444 (tp-100) cc_final: 0.9072 (tp-100) REVERT: C 88 ARG cc_start: 0.9098 (mmt90) cc_final: 0.8710 (mmt90) REVERT: C 111 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8145 (mm) REVERT: D 42 TYR cc_start: 0.7936 (t80) cc_final: 0.7631 (t80) REVERT: D 47 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8931 (tm-30) REVERT: D 57 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8378 (mmmm) REVERT: D 68 ASP cc_start: 0.9130 (t0) cc_final: 0.8760 (t0) REVERT: D 83 TYR cc_start: 0.8541 (t80) cc_final: 0.8059 (t80) REVERT: D 105 GLU cc_start: 0.8961 (tp30) cc_final: 0.8527 (tp30) REVERT: E 76 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8823 (pp30) REVERT: F 53 GLU cc_start: 0.9241 (tp30) cc_final: 0.8979 (tp30) REVERT: F 63 GLU cc_start: 0.9233 (tt0) cc_final: 0.8792 (mt-10) REVERT: F 74 GLU cc_start: 0.9447 (tp30) cc_final: 0.9212 (tp30) REVERT: F 84 MET cc_start: 0.9023 (mmm) cc_final: 0.8597 (mmm) REVERT: F 85 ASP cc_start: 0.8947 (m-30) cc_final: 0.8506 (m-30) REVERT: G 24 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8529 (mm110) REVERT: G 35 ARG cc_start: 0.9439 (mtm110) cc_final: 0.8770 (mtm-85) REVERT: G 59 THR cc_start: 0.9274 (m) cc_final: 0.8962 (t) REVERT: G 73 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9064 (t0) REVERT: G 75 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8181 (mmmm) REVERT: G 90 ASP cc_start: 0.8124 (t0) cc_final: 0.7907 (t0) REVERT: G 100 VAL cc_start: 0.9702 (t) cc_final: 0.9274 (p) REVERT: H 68 ASP cc_start: 0.9119 (t0) cc_final: 0.8818 (t0) REVERT: H 113 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8472 (tm-30) outliers start: 31 outliers final: 18 residues processed: 237 average time/residue: 0.2862 time to fit residues: 91.2315 Evaluate side-chains 235 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN 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 B residue 71 THR Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 73 ASN 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 9 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042496 restraints weight = 46668.581| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.48 r_work: 0.2610 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12684 Z= 0.182 Angle : 0.601 7.452 18373 Z= 0.350 Chirality : 0.034 0.161 2090 Planarity : 0.004 0.036 1320 Dihedral : 30.946 177.734 3997 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.47 % Allowed : 30.51 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.31), residues: 734 helix: 2.01 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.68 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE B 100 TYR 0.034 0.002 TYR D 40 ARG 0.007 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 767) hydrogen bonds : angle 2.94672 ( 1931) covalent geometry : bond 0.00411 (12684) covalent geometry : angle 0.60051 (18373) *********************** 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 253 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8586 (pm20) cc_final: 0.8242 (pm20) REVERT: A 68 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8880 (tt0) REVERT: A 76 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8697 (tm-30) REVERT: A 94 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8733 (tp30) REVERT: A 133 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: B 27 GLN cc_start: 0.8765 (pt0) cc_final: 0.8448 (pm20) REVERT: B 53 GLU cc_start: 0.8782 (tp30) cc_final: 0.8113 (tp30) REVERT: B 84 MET cc_start: 0.8845 (tpp) cc_final: 0.8150 (tpp) REVERT: B 88 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 92 ARG cc_start: 0.9343 (ttp80) cc_final: 0.8856 (ttp80) REVERT: C 61 GLU cc_start: 0.8996 (tp30) cc_final: 0.8555 (tp30) REVERT: C 64 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.9032 (pp20) REVERT: C 84 GLN cc_start: 0.9467 (tp-100) cc_final: 0.9164 (tp-100) REVERT: C 88 ARG cc_start: 0.9115 (mmt90) cc_final: 0.8798 (mmt90) REVERT: C 95 LYS cc_start: 0.9331 (ttmt) cc_final: 0.8995 (tmmt) REVERT: C 111 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8071 (mm) REVERT: D 42 TYR cc_start: 0.7965 (t80) cc_final: 0.7687 (t80) REVERT: D 47 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8898 (tm-30) REVERT: D 57 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8352 (mmmm) REVERT: D 68 ASP cc_start: 0.9128 (t0) cc_final: 0.8756 (t0) REVERT: D 80 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9025 (mp) REVERT: D 83 TYR cc_start: 0.8475 (t80) cc_final: 0.8041 (t80) REVERT: D 105 GLU cc_start: 0.8941 (tp30) cc_final: 0.8320 (tp30) REVERT: E 76 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8839 (pp30) REVERT: F 53 GLU cc_start: 0.9234 (tp30) cc_final: 0.8952 (tp30) REVERT: F 63 GLU cc_start: 0.9236 (tt0) cc_final: 0.8819 (mt-10) REVERT: F 84 MET cc_start: 0.9007 (mmm) cc_final: 0.8557 (mmm) REVERT: F 85 ASP cc_start: 0.8891 (m-30) cc_final: 0.8653 (m-30) REVERT: G 35 ARG cc_start: 0.9429 (mtm110) cc_final: 0.8749 (mtm-85) REVERT: G 56 GLU cc_start: 0.8903 (tt0) cc_final: 0.8549 (tp30) REVERT: G 73 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9043 (t0) REVERT: G 75 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8213 (mmmm) REVERT: G 90 ASP cc_start: 0.8016 (t0) cc_final: 0.7611 (t0) REVERT: G 91 GLU cc_start: 0.8738 (tp30) cc_final: 0.8504 (tp30) REVERT: G 92 GLU cc_start: 0.9341 (mp0) cc_final: 0.9067 (mt-10) REVERT: G 100 VAL cc_start: 0.9692 (t) cc_final: 0.9266 (p) REVERT: H 68 ASP cc_start: 0.9112 (t0) cc_final: 0.8841 (t0) REVERT: H 82 HIS cc_start: 0.9363 (t70) cc_final: 0.9141 (t70) REVERT: H 113 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8466 (tm-30) outliers start: 28 outliers final: 16 residues processed: 243 average time/residue: 0.2660 time to fit residues: 87.4058 Evaluate side-chains 237 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN 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 A residue 133 GLU Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 76 GLN 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 62 ILE Chi-restraints excluded: chain G residue 73 ASN 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 18 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.057387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.042720 restraints weight = 47197.543| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.51 r_work: 0.2619 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12684 Z= 0.179 Angle : 0.609 7.817 18373 Z= 0.354 Chirality : 0.034 0.208 2090 Planarity : 0.004 0.034 1320 Dihedral : 30.919 177.747 3997 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.83 % Allowed : 30.99 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.31), residues: 734 helix: 2.10 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.62 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE B 100 TYR 0.014 0.002 TYR C 50 ARG 0.007 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 767) hydrogen bonds : angle 2.92574 ( 1931) covalent geometry : bond 0.00402 (12684) covalent geometry : angle 0.60934 (18373) *********************** 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 243 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8586 (pm20) cc_final: 0.8245 (pm20) REVERT: A 68 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8884 (tt0) REVERT: A 94 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8747 (tp30) REVERT: A 133 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: B 27 GLN cc_start: 0.8732 (pt0) cc_final: 0.8379 (pm20) REVERT: B 53 GLU cc_start: 0.8765 (tp30) cc_final: 0.8163 (tp30) REVERT: B 84 MET cc_start: 0.8848 (tpp) cc_final: 0.8125 (tpp) REVERT: B 88 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: B 92 ARG cc_start: 0.9362 (ttp80) cc_final: 0.8864 (ttp80) REVERT: C 61 GLU cc_start: 0.8991 (tp30) cc_final: 0.8536 (tp30) REVERT: C 64 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9038 (pp20) REVERT: C 84 GLN cc_start: 0.9414 (tp-100) cc_final: 0.9155 (tp-100) REVERT: C 88 ARG cc_start: 0.9101 (mmt90) cc_final: 0.8835 (mmt90) REVERT: C 95 LYS cc_start: 0.9314 (ttmt) cc_final: 0.8973 (tmmt) REVERT: C 111 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8054 (mm) REVERT: D 42 TYR cc_start: 0.7965 (t80) cc_final: 0.7652 (t80) REVERT: D 47 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8914 (tm-30) REVERT: D 68 ASP cc_start: 0.9127 (t0) cc_final: 0.8746 (t0) REVERT: D 83 TYR cc_start: 0.8496 (t80) cc_final: 0.8035 (t80) REVERT: D 105 GLU cc_start: 0.8926 (tp30) cc_final: 0.8313 (tp30) REVERT: E 76 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8829 (pp30) REVERT: F 53 GLU cc_start: 0.9208 (tp30) cc_final: 0.8904 (tp30) REVERT: F 63 GLU cc_start: 0.9247 (tt0) cc_final: 0.8833 (mt-10) REVERT: F 84 MET cc_start: 0.9045 (mmm) cc_final: 0.8257 (mmm) REVERT: G 73 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.9039 (t0) REVERT: G 75 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8213 (mmmm) REVERT: G 90 ASP cc_start: 0.8026 (t0) cc_final: 0.7732 (t0) REVERT: G 100 VAL cc_start: 0.9690 (t) cc_final: 0.9254 (p) REVERT: H 68 ASP cc_start: 0.9124 (t0) cc_final: 0.8856 (t0) REVERT: H 82 HIS cc_start: 0.9376 (t70) cc_final: 0.9149 (t70) REVERT: H 113 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8497 (tm-30) outliers start: 24 outliers final: 17 residues processed: 234 average time/residue: 0.2765 time to fit residues: 87.6000 Evaluate side-chains 236 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 GLN 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 A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN 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 58 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043965 restraints weight = 46507.550| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.52 r_work: 0.2655 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12684 Z= 0.160 Angle : 0.605 8.436 18373 Z= 0.351 Chirality : 0.033 0.198 2090 Planarity : 0.004 0.032 1320 Dihedral : 30.843 177.725 3997 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.72 % Allowed : 33.07 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.31), residues: 734 helix: 2.13 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.56 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE D 70 TYR 0.028 0.002 TYR D 40 ARG 0.008 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 767) hydrogen bonds : angle 2.90818 ( 1931) covalent geometry : bond 0.00355 (12684) covalent geometry : angle 0.60537 (18373) *********************** 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 244 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8590 (pm20) cc_final: 0.8228 (pm20) REVERT: A 60 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8874 (tp) REVERT: A 94 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8668 (tp30) REVERT: B 27 GLN cc_start: 0.8742 (pt0) cc_final: 0.8438 (pm20) REVERT: B 53 GLU cc_start: 0.8746 (tp30) cc_final: 0.8261 (tp30) REVERT: B 84 MET cc_start: 0.8803 (tpp) cc_final: 0.8138 (tpp) REVERT: B 88 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: B 92 ARG cc_start: 0.9357 (ttp80) cc_final: 0.8862 (ttp80) REVERT: C 61 GLU cc_start: 0.8977 (tp30) cc_final: 0.8505 (tp30) REVERT: C 64 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.9020 (pp20) REVERT: C 84 GLN cc_start: 0.9403 (tp-100) cc_final: 0.9137 (tp-100) REVERT: C 88 ARG cc_start: 0.9106 (mmt90) cc_final: 0.8800 (mmt90) REVERT: C 95 LYS cc_start: 0.9280 (ttmt) cc_final: 0.8951 (tmmt) REVERT: D 42 TYR cc_start: 0.7830 (t80) cc_final: 0.7567 (t80) REVERT: D 68 ASP cc_start: 0.9143 (t0) cc_final: 0.8787 (t0) REVERT: D 83 TYR cc_start: 0.8453 (t80) cc_final: 0.8037 (t80) REVERT: D 105 GLU cc_start: 0.8850 (tp30) cc_final: 0.8234 (tp30) REVERT: E 73 GLU cc_start: 0.8729 (tp30) cc_final: 0.8479 (tp30) REVERT: E 76 GLN cc_start: 0.9166 (pp30) cc_final: 0.8833 (pp30) REVERT: F 63 GLU cc_start: 0.9240 (tt0) cc_final: 0.8817 (mt-10) REVERT: F 84 MET cc_start: 0.8927 (mmm) cc_final: 0.8329 (mmm) REVERT: F 88 TYR cc_start: 0.8659 (m-10) cc_final: 0.8438 (m-80) REVERT: G 56 GLU cc_start: 0.8861 (tt0) cc_final: 0.8458 (tt0) REVERT: G 73 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.9010 (t0) REVERT: G 90 ASP cc_start: 0.7913 (t0) cc_final: 0.7582 (t0) REVERT: G 100 VAL cc_start: 0.9683 (t) cc_final: 0.9244 (p) REVERT: H 68 ASP cc_start: 0.9072 (t0) cc_final: 0.8865 (t0) REVERT: H 82 HIS cc_start: 0.9348 (t70) cc_final: 0.9119 (t70) REVERT: H 113 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8512 (tm-30) outliers start: 17 outliers final: 10 residues processed: 235 average time/residue: 0.2879 time to fit residues: 91.0145 Evaluate side-chains 233 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 73 ASN 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 73 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 93 GLN ** E 108 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 = 0.3225 r_free = 0.3225 target = 0.056110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.041034 restraints weight = 46822.651| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.49 r_work: 0.2576 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 12684 Z= 0.269 Angle : 0.666 8.859 18373 Z= 0.380 Chirality : 0.037 0.197 2090 Planarity : 0.005 0.050 1320 Dihedral : 31.131 177.227 3997 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.04 % Allowed : 33.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.31), residues: 734 helix: 2.08 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.70 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE C 25 TYR 0.037 0.002 TYR D 40 ARG 0.008 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 767) hydrogen bonds : angle 3.16555 ( 1931) covalent geometry : bond 0.00617 (12684) covalent geometry : angle 0.66561 (18373) ********************** 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 225 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8617 (pm20) cc_final: 0.8262 (pm20) REVERT: A 94 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8749 (tp30) REVERT: A 133 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: B 27 GLN cc_start: 0.8735 (pt0) cc_final: 0.8388 (pm20) REVERT: B 53 GLU cc_start: 0.8870 (tp30) cc_final: 0.8226 (tp30) REVERT: B 84 MET cc_start: 0.8928 (tpp) cc_final: 0.8121 (tpp) REVERT: B 88 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: B 92 ARG cc_start: 0.9369 (ttp80) cc_final: 0.8846 (ttp80) REVERT: C 61 GLU cc_start: 0.9053 (tp30) cc_final: 0.8624 (tp30) REVERT: C 64 GLU cc_start: 0.9376 (pp20) cc_final: 0.9020 (pp20) REVERT: C 88 ARG cc_start: 0.9113 (mmt90) cc_final: 0.8841 (mmt90) REVERT: C 111 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8146 (mm) REVERT: D 42 TYR cc_start: 0.7934 (t80) cc_final: 0.7679 (t80) REVERT: D 68 ASP cc_start: 0.9148 (t0) cc_final: 0.8770 (t0) REVERT: D 76 GLU cc_start: 0.9062 (tp30) cc_final: 0.8851 (tp30) REVERT: D 83 TYR cc_start: 0.8646 (t80) cc_final: 0.8063 (t80) REVERT: D 105 GLU cc_start: 0.8970 (tp30) cc_final: 0.8519 (tp30) REVERT: E 76 GLN cc_start: 0.9139 (pp30) cc_final: 0.8848 (pp30) REVERT: F 63 GLU cc_start: 0.9283 (tt0) cc_final: 0.8678 (mt-10) REVERT: F 84 MET cc_start: 0.9034 (mmm) cc_final: 0.8499 (mmm) REVERT: F 85 ASP cc_start: 0.9014 (m-30) cc_final: 0.8586 (m-30) REVERT: G 56 GLU cc_start: 0.8913 (tt0) cc_final: 0.8344 (tt0) REVERT: G 59 THR cc_start: 0.9359 (m) cc_final: 0.9124 (t) REVERT: G 73 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.9093 (t0) REVERT: G 75 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8251 (mmmm) REVERT: G 90 ASP cc_start: 0.8246 (t0) cc_final: 0.7938 (t0) REVERT: G 100 VAL cc_start: 0.9718 (t) cc_final: 0.9290 (p) REVERT: H 68 ASP cc_start: 0.9128 (t0) cc_final: 0.8805 (t0) REVERT: H 113 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8473 (tm-30) outliers start: 19 outliers final: 12 residues processed: 219 average time/residue: 0.2975 time to fit residues: 88.2555 Evaluate side-chains 220 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 73 ASN 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 81 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.040375 restraints weight = 47509.804| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.64 r_work: 0.2529 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 12684 Z= 0.242 Angle : 0.664 8.784 18373 Z= 0.379 Chirality : 0.036 0.202 2090 Planarity : 0.004 0.044 1320 Dihedral : 31.096 177.219 3997 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.88 % Allowed : 33.55 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.31), residues: 734 helix: 2.16 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.80 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE B 100 TYR 0.023 0.002 TYR D 40 ARG 0.008 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 767) hydrogen bonds : angle 3.16093 ( 1931) covalent geometry : bond 0.00554 (12684) covalent geometry : angle 0.66446 (18373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5993.63 seconds wall clock time: 105 minutes 41.10 seconds (6341.10 seconds total)