Starting phenix.real_space_refine on Sat Aug 23 10:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbx_36148/08_2025/8jbx_36148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbx_36148/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2025/8jbx_36148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2025/8jbx_36148_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2025/8jbx_36148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbx_36148/08_2025/8jbx_36148.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 14 5.16 5 C 6564 2.51 5 N 2227 2.21 5 O 2788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11881 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.93, per 1000 atoms: 0.25 Number of scatterers: 11881 At special positions: 0 Unit cell: (75.26, 118.72, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 288 15.00 O 2788 8.00 N 2227 7.00 C 6564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 363.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 72.7% alpha, 2.7% beta 142 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.751A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.644A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.300A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.422A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.832A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.554A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.522A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.692A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.629A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.330A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 38 through 49 removed outlier: 3.612A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 83 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.422A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.390A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.712A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.252A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.525A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 403 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 0.96 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.32), residues: 734 helix: 1.91 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -1.08 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.024 0.002 TYR D 121 PHE 0.007 0.001 PHE E 78 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00387 (12684) covalent geometry : angle 0.58389 (18373) hydrogen bonds : bond 0.09436 ( 767) hydrogen bonds : angle 3.58959 ( 1931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 269 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 87 SER cc_start: 0.9548 (p) cc_final: 0.9231 (t) REVERT: A 94 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8435 (tp30) REVERT: A 125 GLN cc_start: 0.9096 (mt0) cc_final: 0.8832 (mt0) REVERT: D 42 TYR cc_start: 0.7666 (t80) cc_final: 0.7155 (t80) REVERT: D 68 ASP cc_start: 0.9156 (t0) cc_final: 0.8905 (t0) REVERT: D 89 ILE cc_start: 0.9181 (mm) cc_final: 0.8864 (mm) REVERT: E 74 ILE cc_start: 0.9535 (tt) cc_final: 0.9303 (tt) REVERT: E 76 GLN cc_start: 0.9055 (pp30) cc_final: 0.8822 (pp30) REVERT: E 108 ASN cc_start: 0.9476 (t0) cc_final: 0.9140 (t0) REVERT: F 63 GLU cc_start: 0.8866 (tt0) cc_final: 0.8620 (mt-10) REVERT: F 80 THR cc_start: 0.9432 (t) cc_final: 0.8985 (p) REVERT: G 35 ARG cc_start: 0.9079 (mtm110) cc_final: 0.8755 (mtm-85) REVERT: G 59 THR cc_start: 0.9519 (m) cc_final: 0.9302 (t) REVERT: G 71 ARG cc_start: 0.9184 (ttp-110) cc_final: 0.8769 (ttp-110) REVERT: G 100 VAL cc_start: 0.9353 (t) cc_final: 0.9108 (p) REVERT: G 101 THR cc_start: 0.9279 (m) cc_final: 0.8909 (t) REVERT: H 45 LEU cc_start: 0.9633 (tp) cc_final: 0.9384 (tt) REVERT: H 113 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8181 (tm-30) outliers start: 3 outliers final: 0 residues processed: 270 average time/residue: 0.1303 time to fit residues: 46.1049 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 : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3253 r_free = 0.3253 target = 0.057457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042250 restraints weight = 46125.693| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.42 r_work: 0.2602 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1641 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= 0.244 Angle : 0.621 7.858 18373 Z= 0.362 Chirality : 0.036 0.169 2090 Planarity : 0.004 0.055 1320 Dihedral : 30.859 177.974 3997 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.47 % Allowed : 26.84 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG H 33 TYR 0.015 0.002 TYR C 39 PHE 0.008 0.001 PHE B 100 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00547 (12684) covalent geometry : angle 0.62128 (18373) hydrogen bonds : bond 0.04229 ( 767) hydrogen bonds : angle 3.03474 ( 1931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8443 (pm20) cc_final: 0.8223 (pm20) REVERT: A 76 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 87 SER cc_start: 0.9419 (p) cc_final: 0.9214 (t) REVERT: A 94 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8674 (tp30) REVERT: B 27 GLN cc_start: 0.8644 (pt0) cc_final: 0.8355 (pm20) REVERT: B 31 LYS cc_start: 0.9450 (tttt) cc_final: 0.9129 (tttp) REVERT: B 53 GLU cc_start: 0.8793 (tp30) cc_final: 0.8069 (tp30) REVERT: B 84 MET cc_start: 0.8985 (tpp) cc_final: 0.8420 (tpt) REVERT: B 92 ARG cc_start: 0.9433 (ttp80) cc_final: 0.9029 (ttp80) REVERT: C 99 ARG cc_start: 0.8878 (tpp80) cc_final: 0.8676 (tpp80) REVERT: D 42 TYR cc_start: 0.7899 (t80) cc_final: 0.7514 (t80) REVERT: D 47 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8891 (tm-30) REVERT: D 68 ASP cc_start: 0.9125 (t0) cc_final: 0.8785 (t0) REVERT: D 79 ARG cc_start: 0.9364 (mtm180) cc_final: 0.9121 (ttp-110) REVERT: D 89 ILE cc_start: 0.9000 (mm) cc_final: 0.8687 (mm) REVERT: D 105 GLU cc_start: 0.8952 (tp30) cc_final: 0.8166 (tp30) REVERT: E 42 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7951 (ttm110) REVERT: E 74 ILE cc_start: 0.9161 (tt) cc_final: 0.8942 (tt) REVERT: E 76 GLN cc_start: 0.9186 (pp30) cc_final: 0.8843 (pp30) REVERT: E 108 ASN cc_start: 0.9513 (t0) cc_final: 0.9242 (t0) REVERT: F 63 GLU cc_start: 0.9169 (tt0) cc_final: 0.8823 (mt-10) REVERT: G 35 ARG cc_start: 0.9435 (mtm110) cc_final: 0.8789 (mtm-85) REVERT: G 59 THR cc_start: 0.9300 (m) cc_final: 0.9021 (t) REVERT: G 73 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.8971 (t0) REVERT: G 100 VAL cc_start: 0.9667 (t) cc_final: 0.9143 (p) REVERT: G 101 THR cc_start: 0.9091 (m) cc_final: 0.8595 (t) REVERT: H 105 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8065 (mm-30) REVERT: H 113 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8387 (tm-30) outliers start: 28 outliers final: 16 residues processed: 247 average time/residue: 0.1217 time to fit residues: 40.1486 Evaluate side-chains 234 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.058153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043004 restraints weight = 46573.536| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.46 r_work: 0.2611 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12684 Z= 0.197 Angle : 0.602 6.845 18373 Z= 0.351 Chirality : 0.034 0.162 2090 Planarity : 0.004 0.044 1320 Dihedral : 30.863 177.639 3997 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.63 % Allowed : 28.75 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.31), residues: 734 helix: 2.05 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.93 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.019 0.002 TYR H 40 PHE 0.008 0.001 PHE B 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00445 (12684) covalent geometry : angle 0.60152 (18373) hydrogen bonds : bond 0.03821 ( 767) hydrogen bonds : angle 2.96904 ( 1931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8513 (pm20) cc_final: 0.8223 (pm20) REVERT: A 76 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 87 SER cc_start: 0.9384 (p) cc_final: 0.9163 (t) REVERT: A 94 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8666 (tp30) REVERT: B 27 GLN cc_start: 0.8653 (pt0) cc_final: 0.8360 (pm20) REVERT: B 31 LYS cc_start: 0.9445 (tttt) cc_final: 0.9151 (tttp) REVERT: B 53 GLU cc_start: 0.8763 (tp30) cc_final: 0.8175 (tp30) REVERT: B 84 MET cc_start: 0.8932 (tpp) cc_final: 0.8503 (tpt) REVERT: B 92 ARG cc_start: 0.9459 (ttp80) cc_final: 0.9014 (ttp80) REVERT: C 61 GLU cc_start: 0.8908 (tp30) cc_final: 0.8516 (tp30) REVERT: C 64 GLU cc_start: 0.9339 (pp20) cc_final: 0.9017 (pp20) REVERT: C 84 GLN cc_start: 0.9509 (tp-100) cc_final: 0.9282 (tp-100) REVERT: D 42 TYR cc_start: 0.7889 (t80) cc_final: 0.7491 (t80) REVERT: D 47 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8914 (tm-30) REVERT: D 68 ASP cc_start: 0.9142 (t0) cc_final: 0.8809 (t0) REVERT: D 105 GLU cc_start: 0.8940 (tp30) cc_final: 0.8400 (tp30) REVERT: E 72 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8043 (mtt90) REVERT: E 74 ILE cc_start: 0.9187 (tt) cc_final: 0.8938 (tt) REVERT: E 76 GLN cc_start: 0.9184 (pp30) cc_final: 0.8817 (pp30) REVERT: E 108 ASN cc_start: 0.9518 (t0) cc_final: 0.9294 (t0) REVERT: F 63 GLU cc_start: 0.9168 (tt0) cc_final: 0.8812 (mt-10) REVERT: F 72 TYR cc_start: 0.8995 (m-80) cc_final: 0.8757 (m-80) REVERT: F 85 ASP cc_start: 0.8963 (m-30) cc_final: 0.8638 (m-30) REVERT: G 59 THR cc_start: 0.9286 (m) cc_final: 0.8968 (t) REVERT: G 73 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.8975 (t0) REVERT: G 90 ASP cc_start: 0.8069 (t0) cc_final: 0.7864 (t0) REVERT: G 100 VAL cc_start: 0.9657 (t) cc_final: 0.9188 (p) REVERT: G 101 THR cc_start: 0.9170 (m) cc_final: 0.8672 (t) REVERT: H 113 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8383 (tm-30) outliers start: 29 outliers final: 16 residues processed: 244 average time/residue: 0.1159 time to fit residues: 38.1223 Evaluate side-chains 230 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 71 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 109 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 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 96 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 0.0030 chunk 77 optimal weight: 7.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.058606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043528 restraints weight = 46157.488| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.45 r_work: 0.2631 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12684 Z= 0.179 Angle : 0.587 6.615 18373 Z= 0.344 Chirality : 0.034 0.158 2090 Planarity : 0.004 0.043 1320 Dihedral : 30.826 177.935 3997 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.83 % Allowed : 29.55 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.31), residues: 734 helix: 2.04 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.77 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.020 0.002 TYR H 40 PHE 0.008 0.001 PHE B 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (12684) covalent geometry : angle 0.58710 (18373) hydrogen bonds : bond 0.03679 ( 767) hydrogen bonds : angle 2.89630 ( 1931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8527 (pm20) cc_final: 0.8216 (pm20) REVERT: A 68 GLN cc_start: 0.9098 (tt0) cc_final: 0.8882 (tt0) REVERT: A 76 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 87 SER cc_start: 0.9350 (p) cc_final: 0.9116 (t) REVERT: A 94 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8623 (tp30) REVERT: B 27 GLN cc_start: 0.8692 (pt0) cc_final: 0.8353 (pm20) REVERT: B 31 LYS cc_start: 0.9446 (tttt) cc_final: 0.9170 (tttp) REVERT: B 84 MET cc_start: 0.8970 (tpp) cc_final: 0.8550 (tpp) REVERT: B 92 ARG cc_start: 0.9436 (ttp80) cc_final: 0.9000 (ttp80) REVERT: C 38 ASN cc_start: 0.8545 (p0) cc_final: 0.8251 (p0) REVERT: C 61 GLU cc_start: 0.8974 (tp30) cc_final: 0.8542 (tp30) REVERT: C 64 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.8974 (pp20) REVERT: C 84 GLN cc_start: 0.9511 (tp-100) cc_final: 0.9158 (tp-100) REVERT: C 88 ARG cc_start: 0.9059 (mmt90) cc_final: 0.8785 (mmt90) REVERT: D 42 TYR cc_start: 0.7852 (t80) cc_final: 0.7488 (t80) REVERT: D 47 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8883 (tm-30) REVERT: D 68 ASP cc_start: 0.9138 (t0) cc_final: 0.8771 (t0) REVERT: D 105 GLU cc_start: 0.8898 (tp30) cc_final: 0.8410 (tp30) REVERT: E 72 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8069 (mtt90) REVERT: E 74 ILE cc_start: 0.9194 (tt) cc_final: 0.8927 (tt) REVERT: E 76 GLN cc_start: 0.9149 (pp30) cc_final: 0.8772 (pp30) REVERT: E 108 ASN cc_start: 0.9509 (t0) cc_final: 0.9249 (t0) REVERT: F 53 GLU cc_start: 0.9212 (tp30) cc_final: 0.8991 (tp30) REVERT: F 63 GLU cc_start: 0.9134 (tt0) cc_final: 0.8770 (mt-10) REVERT: F 84 MET cc_start: 0.8809 (mmm) cc_final: 0.8553 (tmm) REVERT: F 85 ASP cc_start: 0.8912 (m-30) cc_final: 0.8552 (m-30) REVERT: G 59 THR cc_start: 0.9289 (m) cc_final: 0.8963 (t) REVERT: G 73 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.8999 (t0) REVERT: G 75 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8644 (mmmm) REVERT: G 90 ASP cc_start: 0.8085 (t0) cc_final: 0.7773 (t0) REVERT: G 100 VAL cc_start: 0.9657 (t) cc_final: 0.9172 (p) REVERT: G 101 THR cc_start: 0.9203 (m) cc_final: 0.8717 (t) REVERT: H 113 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8444 (tm-30) outliers start: 24 outliers final: 15 residues processed: 246 average time/residue: 0.1147 time to fit residues: 38.1290 Evaluate side-chains 233 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 86 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 D 63 ASN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.044862 restraints weight = 45760.198| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.47 r_work: 0.2671 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12684 Z= 0.157 Angle : 0.577 6.561 18373 Z= 0.339 Chirality : 0.033 0.160 2090 Planarity : 0.004 0.035 1320 Dihedral : 30.743 177.813 3997 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.15 % Allowed : 30.35 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.31), residues: 734 helix: 2.19 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.78 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.023 0.002 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00348 (12684) covalent geometry : angle 0.57726 (18373) hydrogen bonds : bond 0.03516 ( 767) hydrogen bonds : angle 2.85460 ( 1931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8467 (pm20) cc_final: 0.8107 (pm20) REVERT: A 60 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 68 GLN cc_start: 0.9075 (tt0) cc_final: 0.8860 (tt0) REVERT: A 87 SER cc_start: 0.9326 (p) cc_final: 0.9076 (t) REVERT: A 94 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8565 (tp30) REVERT: B 27 GLN cc_start: 0.8701 (pt0) cc_final: 0.8368 (pm20) REVERT: B 31 LYS cc_start: 0.9446 (tttt) cc_final: 0.9159 (tttp) REVERT: B 53 GLU cc_start: 0.8570 (tp30) cc_final: 0.8165 (tm-30) REVERT: B 84 MET cc_start: 0.9062 (tpp) cc_final: 0.8664 (tpp) REVERT: B 92 ARG cc_start: 0.9375 (ttp80) cc_final: 0.8962 (ttp80) REVERT: C 39 TYR cc_start: 0.8468 (m-10) cc_final: 0.8243 (m-10) REVERT: C 61 GLU cc_start: 0.8961 (tp30) cc_final: 0.8519 (tp30) REVERT: C 64 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.8991 (pp20) REVERT: C 84 GLN cc_start: 0.9472 (tp-100) cc_final: 0.9158 (tp-100) REVERT: C 88 ARG cc_start: 0.9065 (mmt90) cc_final: 0.8806 (mmt90) REVERT: D 42 TYR cc_start: 0.7857 (t80) cc_final: 0.7547 (t80) REVERT: D 68 ASP cc_start: 0.9154 (t0) cc_final: 0.8810 (t0) REVERT: D 105 GLU cc_start: 0.8859 (tp30) cc_final: 0.8356 (tp30) REVERT: E 72 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8054 (mtt90) REVERT: E 73 GLU cc_start: 0.8814 (tp30) cc_final: 0.8597 (tp30) REVERT: E 76 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8742 (pp30) REVERT: E 108 ASN cc_start: 0.9472 (t0) cc_final: 0.9195 (t0) REVERT: E 125 GLN cc_start: 0.8865 (mt0) cc_final: 0.8588 (mt0) REVERT: F 74 GLU cc_start: 0.9461 (tp30) cc_final: 0.9102 (tp30) REVERT: G 24 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8906 (mm-40) REVERT: G 59 THR cc_start: 0.9266 (m) cc_final: 0.8946 (t) REVERT: G 73 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.9012 (t0) REVERT: G 75 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8637 (mmmm) REVERT: G 90 ASP cc_start: 0.8003 (t0) cc_final: 0.7645 (t0) REVERT: G 100 VAL cc_start: 0.9641 (t) cc_final: 0.9196 (p) REVERT: H 82 HIS cc_start: 0.9238 (t70) cc_final: 0.8991 (t70) REVERT: H 113 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8511 (tm-30) outliers start: 26 outliers final: 14 residues processed: 251 average time/residue: 0.1166 time to fit residues: 39.8661 Evaluate side-chains 243 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 108 LYS 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 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 73 ASN 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 25 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 D 63 ASN E 93 GLN F 25 ASN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.043166 restraints weight = 46602.284| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.50 r_work: 0.2633 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12684 Z= 0.205 Angle : 0.606 6.588 18373 Z= 0.353 Chirality : 0.035 0.210 2090 Planarity : 0.004 0.047 1320 Dihedral : 30.875 177.743 3997 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.63 % Allowed : 30.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.31), residues: 734 helix: 2.14 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.64 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 92 TYR 0.040 0.002 TYR D 40 PHE 0.007 0.001 PHE B 100 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00468 (12684) covalent geometry : angle 0.60567 (18373) hydrogen bonds : bond 0.03785 ( 767) hydrogen bonds : angle 2.95733 ( 1931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8472 (pm20) cc_final: 0.8097 (pm20) REVERT: A 87 SER cc_start: 0.9354 (p) cc_final: 0.9123 (t) REVERT: A 94 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8717 (tp30) REVERT: B 27 GLN cc_start: 0.8716 (pt0) cc_final: 0.8344 (pm20) REVERT: B 31 LYS cc_start: 0.9441 (tttt) cc_final: 0.9139 (tttp) REVERT: B 53 GLU cc_start: 0.8610 (tp30) cc_final: 0.8218 (tm-30) REVERT: B 84 MET cc_start: 0.9054 (tpp) cc_final: 0.8795 (tpp) REVERT: B 92 ARG cc_start: 0.9375 (ttp80) cc_final: 0.8927 (ttp80) REVERT: C 61 GLU cc_start: 0.9033 (tp30) cc_final: 0.8589 (tp30) REVERT: C 64 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8991 (pp20) REVERT: D 33 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.8123 (tpp-160) REVERT: D 42 TYR cc_start: 0.7920 (t80) cc_final: 0.7617 (t80) REVERT: D 68 ASP cc_start: 0.9118 (t0) cc_final: 0.8731 (t0) REVERT: D 105 GLU cc_start: 0.8920 (tp30) cc_final: 0.8467 (tp30) REVERT: E 72 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8048 (mtt90) REVERT: E 76 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8770 (pp30) REVERT: E 125 GLN cc_start: 0.8911 (mt0) cc_final: 0.8600 (mt0) REVERT: F 63 GLU cc_start: 0.9181 (tt0) cc_final: 0.8858 (mt-10) REVERT: G 24 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8975 (mm-40) REVERT: G 73 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8986 (t0) REVERT: G 90 ASP cc_start: 0.8157 (t0) cc_final: 0.7670 (t0) REVERT: G 91 GLU cc_start: 0.8767 (tp30) cc_final: 0.8538 (tp30) REVERT: G 92 GLU cc_start: 0.9383 (mp0) cc_final: 0.9019 (tt0) REVERT: G 100 VAL cc_start: 0.9675 (t) cc_final: 0.9185 (p) REVERT: G 101 THR cc_start: 0.9243 (m) cc_final: 0.8754 (t) REVERT: H 82 HIS cc_start: 0.9274 (t70) cc_final: 0.9051 (t70) REVERT: H 113 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8404 (tm-30) outliers start: 29 outliers final: 17 residues processed: 229 average time/residue: 0.1234 time to fit residues: 38.7111 Evaluate side-chains 225 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 78 SER 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 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 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- 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 D 63 ASN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044067 restraints weight = 46578.132| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.53 r_work: 0.2649 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12684 Z= 0.175 Angle : 0.597 7.212 18373 Z= 0.348 Chirality : 0.033 0.163 2090 Planarity : 0.004 0.036 1320 Dihedral : 30.817 177.672 3997 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.99 % Allowed : 30.67 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.31), residues: 734 helix: 2.11 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.61 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.015 0.002 TYR D 40 PHE 0.007 0.001 PHE B 100 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (12684) covalent geometry : angle 0.59679 (18373) hydrogen bonds : bond 0.03604 ( 767) hydrogen bonds : angle 2.93098 ( 1931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8428 (pm20) cc_final: 0.8054 (pm20) REVERT: A 87 SER cc_start: 0.9342 (p) cc_final: 0.9123 (t) REVERT: A 94 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8696 (tp30) REVERT: B 27 GLN cc_start: 0.8721 (pt0) cc_final: 0.8345 (pm20) REVERT: B 53 GLU cc_start: 0.8601 (tp30) cc_final: 0.8244 (tm-30) REVERT: B 84 MET cc_start: 0.9088 (tpp) cc_final: 0.8782 (tpp) REVERT: B 91 LYS cc_start: 0.9399 (tttm) cc_final: 0.9166 (ttpt) REVERT: B 92 ARG cc_start: 0.9396 (ttp80) cc_final: 0.8929 (ttp80) REVERT: C 61 GLU cc_start: 0.9027 (tp30) cc_final: 0.8569 (tp30) REVERT: C 64 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8978 (pp20) REVERT: C 84 GLN cc_start: 0.9439 (tp-100) cc_final: 0.9205 (tp-100) REVERT: C 88 ARG cc_start: 0.9117 (mmt90) cc_final: 0.8809 (mmt90) REVERT: D 33 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8155 (tpp-160) REVERT: D 42 TYR cc_start: 0.7860 (t80) cc_final: 0.7574 (t80) REVERT: D 68 ASP cc_start: 0.9134 (t0) cc_final: 0.8753 (t0) REVERT: D 105 GLU cc_start: 0.8886 (tp30) cc_final: 0.8362 (tp30) REVERT: E 72 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8033 (mtt90) REVERT: E 73 GLU cc_start: 0.8754 (tp30) cc_final: 0.8502 (tp30) REVERT: E 76 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8802 (pp30) REVERT: G 56 GLU cc_start: 0.8791 (tt0) cc_final: 0.8298 (tp30) REVERT: G 59 THR cc_start: 0.9360 (m) cc_final: 0.9100 (t) REVERT: G 73 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.9007 (t0) REVERT: G 90 ASP cc_start: 0.8098 (t0) cc_final: 0.7597 (t0) REVERT: G 91 GLU cc_start: 0.8756 (tp30) cc_final: 0.8503 (tp30) REVERT: G 92 GLU cc_start: 0.9392 (mp0) cc_final: 0.9041 (tt0) REVERT: G 100 VAL cc_start: 0.9667 (t) cc_final: 0.9227 (p) REVERT: H 113 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8498 (tm-30) outliers start: 25 outliers final: 15 residues processed: 237 average time/residue: 0.1198 time to fit residues: 38.4186 Evaluate side-chains 228 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 66 ILE 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 E residue 72 ARG Chi-restraints excluded: chain E residue 76 GLN 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 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 D 63 ASN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.043275 restraints weight = 46596.528| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.54 r_work: 0.2630 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12684 Z= 0.203 Angle : 0.619 8.433 18373 Z= 0.358 Chirality : 0.034 0.161 2090 Planarity : 0.004 0.036 1320 Dihedral : 30.912 177.531 3997 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.51 % Allowed : 32.75 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.31), residues: 734 helix: 2.07 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.57 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 92 TYR 0.031 0.002 TYR H 40 PHE 0.009 0.001 PHE G 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00460 (12684) covalent geometry : angle 0.61875 (18373) hydrogen bonds : bond 0.03779 ( 767) hydrogen bonds : angle 3.02646 ( 1931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8516 (pm20) cc_final: 0.8146 (pm20) REVERT: A 87 SER cc_start: 0.9366 (p) cc_final: 0.9155 (t) REVERT: A 94 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8722 (tp30) REVERT: A 133 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: B 27 GLN cc_start: 0.8709 (pt0) cc_final: 0.8355 (pm20) REVERT: B 53 GLU cc_start: 0.8624 (tp30) cc_final: 0.8282 (tm-30) REVERT: B 84 MET cc_start: 0.9099 (tpp) cc_final: 0.8803 (tpp) REVERT: B 92 ARG cc_start: 0.9405 (ttp80) cc_final: 0.8948 (ttp80) REVERT: C 61 GLU cc_start: 0.9074 (tp30) cc_final: 0.8630 (tp30) REVERT: C 64 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8988 (pp20) REVERT: C 84 GLN cc_start: 0.9440 (tp-100) cc_final: 0.9115 (tp-100) REVERT: C 88 ARG cc_start: 0.9104 (mmt90) cc_final: 0.8897 (mmt90) REVERT: D 33 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8173 (tpp-160) REVERT: D 42 TYR cc_start: 0.7915 (t80) cc_final: 0.7626 (t80) REVERT: D 68 ASP cc_start: 0.9140 (t0) cc_final: 0.8759 (t0) REVERT: D 105 GLU cc_start: 0.8896 (tp30) cc_final: 0.8461 (tp30) REVERT: E 72 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8054 (mtt90) REVERT: E 73 GLU cc_start: 0.8745 (tp30) cc_final: 0.8485 (tp30) REVERT: E 76 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8807 (pp30) REVERT: F 63 GLU cc_start: 0.9245 (tt0) cc_final: 0.8798 (mt-10) REVERT: G 24 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8976 (mm110) REVERT: G 59 THR cc_start: 0.9366 (m) cc_final: 0.9106 (t) REVERT: G 73 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.8990 (t0) REVERT: G 90 ASP cc_start: 0.8175 (t0) cc_final: 0.7674 (t0) REVERT: G 91 GLU cc_start: 0.8797 (tp30) cc_final: 0.8550 (tp30) REVERT: G 92 GLU cc_start: 0.9401 (mp0) cc_final: 0.9025 (tt0) REVERT: G 100 VAL cc_start: 0.9681 (t) cc_final: 0.9242 (p) REVERT: H 39 VAL cc_start: 0.9410 (m) cc_final: 0.9165 (p) REVERT: H 62 MET cc_start: 0.9498 (tpp) cc_final: 0.9198 (mmm) REVERT: H 113 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8453 (tm-30) outliers start: 22 outliers final: 14 residues processed: 221 average time/residue: 0.1288 time to fit residues: 38.5015 Evaluate side-chains 222 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 83 TYR 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 109 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ** 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 = 0.3281 r_free = 0.3281 target = 0.058685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043815 restraints weight = 46566.141| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.55 r_work: 0.2646 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12684 Z= 0.178 Angle : 0.617 8.235 18373 Z= 0.356 Chirality : 0.033 0.160 2090 Planarity : 0.004 0.035 1320 Dihedral : 30.869 177.597 3997 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.19 % Allowed : 33.87 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.31), residues: 734 helix: 2.04 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.61 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.034 0.002 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (12684) covalent geometry : angle 0.61654 (18373) hydrogen bonds : bond 0.03623 ( 767) hydrogen bonds : angle 2.99091 ( 1931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8544 (pm20) cc_final: 0.8187 (pm20) REVERT: A 87 SER cc_start: 0.9344 (p) cc_final: 0.9120 (t) REVERT: A 94 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8704 (tp30) REVERT: B 27 GLN cc_start: 0.8724 (pt0) cc_final: 0.8369 (pm20) REVERT: B 53 GLU cc_start: 0.8545 (tp30) cc_final: 0.8227 (tm-30) REVERT: B 84 MET cc_start: 0.9109 (tpp) cc_final: 0.8761 (tpp) REVERT: B 92 ARG cc_start: 0.9383 (ttp80) cc_final: 0.8911 (ttp80) REVERT: C 61 GLU cc_start: 0.9053 (tp30) cc_final: 0.8586 (tp30) REVERT: C 64 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.8980 (pp20) REVERT: C 84 GLN cc_start: 0.9442 (tp-100) cc_final: 0.9123 (tp-100) REVERT: C 88 ARG cc_start: 0.9109 (mmt90) cc_final: 0.8894 (mmt90) REVERT: C 95 LYS cc_start: 0.9318 (ttmt) cc_final: 0.8981 (tmmt) REVERT: D 42 TYR cc_start: 0.7880 (t80) cc_final: 0.7643 (t80) REVERT: D 68 ASP cc_start: 0.9146 (t0) cc_final: 0.8777 (t0) REVERT: D 105 GLU cc_start: 0.8872 (tp30) cc_final: 0.8523 (tp30) REVERT: E 72 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8021 (mtt90) REVERT: E 73 GLU cc_start: 0.8697 (tp30) cc_final: 0.8431 (tp30) REVERT: E 76 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8772 (pp30) REVERT: F 63 GLU cc_start: 0.9245 (tt0) cc_final: 0.8825 (mt-10) REVERT: G 24 GLN cc_start: 0.9298 (mm-40) cc_final: 0.9044 (mm110) REVERT: G 56 GLU cc_start: 0.8882 (tt0) cc_final: 0.8449 (tp30) REVERT: G 59 THR cc_start: 0.9345 (m) cc_final: 0.9077 (t) REVERT: G 73 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.8984 (t0) REVERT: G 90 ASP cc_start: 0.8123 (t0) cc_final: 0.7618 (t0) REVERT: G 91 GLU cc_start: 0.8775 (tp30) cc_final: 0.8515 (tp30) REVERT: G 92 GLU cc_start: 0.9410 (mp0) cc_final: 0.9040 (tt0) REVERT: G 100 VAL cc_start: 0.9670 (t) cc_final: 0.9230 (p) REVERT: H 39 VAL cc_start: 0.9372 (m) cc_final: 0.9123 (p) REVERT: H 113 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8495 (tm-30) outliers start: 20 outliers final: 14 residues processed: 228 average time/residue: 0.1233 time to fit residues: 38.7285 Evaluate side-chains 224 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 78 SER 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 109 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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 ** 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 = 0.3275 r_free = 0.3275 target = 0.058389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.043569 restraints weight = 46928.779| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.57 r_work: 0.2640 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12684 Z= 0.193 Angle : 0.628 8.730 18373 Z= 0.360 Chirality : 0.034 0.161 2090 Planarity : 0.004 0.035 1320 Dihedral : 30.902 177.475 3997 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.35 % Allowed : 32.91 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.31), residues: 734 helix: 2.08 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.69 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.022 0.002 TYR F 88 PHE 0.007 0.001 PHE G 25 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00439 (12684) covalent geometry : angle 0.62834 (18373) hydrogen bonds : bond 0.03696 ( 767) hydrogen bonds : angle 3.02255 ( 1931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8530 (pm20) cc_final: 0.8184 (pm20) REVERT: A 68 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8898 (tt0) REVERT: A 87 SER cc_start: 0.9344 (p) cc_final: 0.9086 (t) REVERT: A 94 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8689 (tp30) REVERT: B 27 GLN cc_start: 0.8702 (pt0) cc_final: 0.8363 (pm20) REVERT: B 53 GLU cc_start: 0.8600 (tp30) cc_final: 0.8272 (tm-30) REVERT: B 84 MET cc_start: 0.9123 (tpp) cc_final: 0.8727 (tpp) REVERT: B 92 ARG cc_start: 0.9385 (ttp80) cc_final: 0.8912 (ttp80) REVERT: C 61 GLU cc_start: 0.9056 (tp30) cc_final: 0.8597 (tp30) REVERT: C 64 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8976 (pp20) REVERT: C 84 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9166 (tp-100) REVERT: C 88 ARG cc_start: 0.9123 (mmt90) cc_final: 0.8830 (mmt90) REVERT: D 42 TYR cc_start: 0.7911 (t80) cc_final: 0.7661 (t80) REVERT: D 68 ASP cc_start: 0.9136 (t0) cc_final: 0.8762 (t0) REVERT: D 105 GLU cc_start: 0.8905 (tp30) cc_final: 0.8328 (tp30) REVERT: E 72 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8030 (mtt90) REVERT: E 73 GLU cc_start: 0.8649 (tp30) cc_final: 0.8392 (tp30) REVERT: E 76 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8796 (pp30) REVERT: F 63 GLU cc_start: 0.9260 (tt0) cc_final: 0.8844 (mt-10) REVERT: G 24 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8393 (mp10) REVERT: G 56 GLU cc_start: 0.8895 (tt0) cc_final: 0.8300 (tp30) REVERT: G 59 THR cc_start: 0.9351 (m) cc_final: 0.9072 (t) REVERT: G 73 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.8987 (t0) REVERT: G 90 ASP cc_start: 0.8129 (t0) cc_final: 0.7622 (t0) REVERT: G 91 GLU cc_start: 0.8791 (tp30) cc_final: 0.8533 (tp30) REVERT: G 92 GLU cc_start: 0.9410 (mp0) cc_final: 0.9027 (tt0) REVERT: G 100 VAL cc_start: 0.9679 (t) cc_final: 0.9236 (p) REVERT: H 39 VAL cc_start: 0.9339 (m) cc_final: 0.9109 (p) REVERT: H 46 LYS cc_start: 0.9421 (mmtp) cc_final: 0.9162 (mptt) REVERT: H 113 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8439 (tm-30) outliers start: 21 outliers final: 13 residues processed: 222 average time/residue: 0.1105 time to fit residues: 33.7806 Evaluate side-chains 221 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 78 SER 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 F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 D 63 ASN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044212 restraints weight = 46445.638| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.55 r_work: 0.2663 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12684 Z= 0.173 Angle : 0.628 8.954 18373 Z= 0.360 Chirality : 0.034 0.183 2090 Planarity : 0.004 0.035 1320 Dihedral : 30.865 177.640 3997 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 33.87 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.31), residues: 734 helix: 2.00 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.53 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.023 0.002 TYR F 88 PHE 0.007 0.001 PHE A 67 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00392 (12684) covalent geometry : angle 0.62845 (18373) hydrogen bonds : bond 0.03601 ( 767) hydrogen bonds : angle 3.00224 ( 1931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2456.41 seconds wall clock time: 42 minutes 47.45 seconds (2567.45 seconds total)