Starting phenix.real_space_refine on Sat May 10 02:20:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5o_37299/05_2025/8w5o_37299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5o_37299/05_2025/8w5o_37299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5o_37299/05_2025/8w5o_37299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5o_37299/05_2025/8w5o_37299.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5o_37299/05_2025/8w5o_37299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5o_37299/05_2025/8w5o_37299.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.080 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2924 2.51 5 N 825 2.21 5 O 934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4697 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "b" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 993 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "A" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 975 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Time building chain proxies: 3.30, per 1000 atoms: 0.70 Number of scatterers: 4697 At special positions: 0 Unit cell: (83.16, 112.2, 99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 934 8.00 N 825 7.00 C 2924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 597.4 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 13.9% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.553A pdb=" N TYR H 35 " --> pdb=" O PHE H 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 117 Processing helix chain 'b' and resid 118 through 126 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.518A pdb=" N VAL A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Processing sheet with id=AA1, first strand: chain 'H' and resid 21 through 25 removed outlier: 3.709A pdb=" N CYS H 25 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU H 82 " --> pdb=" O CYS H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 62 removed outlier: 6.714A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.808A pdb=" N LEU L 76 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 56 through 57 removed outlier: 6.919A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS L 52 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE L 36 " --> pdb=" O LYS L 52 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN L 92 " --> pdb=" O HIS L 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 6 through 9 removed outlier: 6.036A pdb=" N SER b 36 " --> pdb=" O PRO b 23 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY b 25 " --> pdb=" O SER b 34 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER b 34 " --> pdb=" O GLY b 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 9 removed outlier: 6.036A pdb=" N SER B 36 " --> pdb=" O PRO B 23 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY B 25 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 34 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 74 removed outlier: 7.075A pdb=" N THR B 72 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR B 85 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 83 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA9, first strand: chain 'A' and resid 34 through 36 143 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 789 1.29 - 1.42: 1174 1.42 - 1.55: 2790 1.55 - 1.68: 7 1.68 - 1.81: 18 Bond restraints: 4778 Sorted by residual: bond pdb=" C VAL A 52 " pdb=" O VAL A 52 " ideal model delta sigma weight residual 1.237 1.160 0.077 1.10e-02 8.26e+03 4.87e+01 bond pdb=" C GLN A 69 " pdb=" O GLN A 69 " ideal model delta sigma weight residual 1.235 1.159 0.076 1.13e-02 7.83e+03 4.58e+01 bond pdb=" C VAL A 64 " pdb=" O VAL A 64 " ideal model delta sigma weight residual 1.238 1.169 0.069 1.06e-02 8.90e+03 4.18e+01 bond pdb=" C GLN L 93 " pdb=" O GLN L 93 " ideal model delta sigma weight residual 1.235 1.157 0.078 1.22e-02 6.72e+03 4.09e+01 bond pdb=" C GLN A 65 " pdb=" O GLN A 65 " ideal model delta sigma weight residual 1.235 1.157 0.077 1.22e-02 6.72e+03 4.02e+01 ... (remaining 4773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.61: 6468 8.61 - 17.21: 28 17.21 - 25.82: 1 25.82 - 34.43: 2 34.43 - 43.03: 1 Bond angle restraints: 6500 Sorted by residual: angle pdb=" C ASP b 81 " pdb=" N PRO b 82 " pdb=" CA PRO b 82 " ideal model delta sigma weight residual 119.84 148.45 -28.61 1.25e+00 6.40e-01 5.24e+02 angle pdb=" C ASP b 81 " pdb=" N PRO b 82 " pdb=" CD PRO b 82 " ideal model delta sigma weight residual 125.00 81.97 43.03 4.10e+00 5.95e-02 1.10e+02 angle pdb=" C ASN A 70 " pdb=" N PRO A 71 " pdb=" CA PRO A 71 " ideal model delta sigma weight residual 119.84 131.98 -12.14 1.25e+00 6.40e-01 9.44e+01 angle pdb=" N ALA A 43 " pdb=" CA ALA A 43 " pdb=" C ALA A 43 " ideal model delta sigma weight residual 112.88 125.25 -12.37 1.29e+00 6.01e-01 9.20e+01 angle pdb=" N LYS A 60 " pdb=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 111.74 123.62 -11.88 1.35e+00 5.49e-01 7.74e+01 ... (remaining 6495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 2617 17.07 - 34.13: 183 34.13 - 51.20: 79 51.20 - 68.26: 18 68.26 - 85.32: 4 Dihedral angle restraints: 2901 sinusoidal: 1111 harmonic: 1790 Sorted by residual: dihedral pdb=" CA ASP H 112 " pdb=" C ASP H 112 " pdb=" N TYR H 113 " pdb=" CA TYR H 113 " ideal model delta harmonic sigma weight residual -180.00 -143.06 -36.94 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" N TRP L 97 " pdb=" C TRP L 97 " pdb=" CA TRP L 97 " pdb=" CB TRP L 97 " ideal model delta harmonic sigma weight residual 122.80 139.62 -16.82 0 2.50e+00 1.60e-01 4.52e+01 dihedral pdb=" C TRP L 97 " pdb=" N TRP L 97 " pdb=" CA TRP L 97 " pdb=" CB TRP L 97 " ideal model delta harmonic sigma weight residual -122.60 -137.70 15.10 0 2.50e+00 1.60e-01 3.65e+01 ... (remaining 2898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 699 0.172 - 0.345: 45 0.345 - 0.517: 11 0.517 - 0.689: 1 0.689 - 0.861: 2 Chirality restraints: 758 Sorted by residual: chirality pdb=" CA TRP L 97 " pdb=" N TRP L 97 " pdb=" C TRP L 97 " pdb=" CB TRP L 97 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" CA GLU H 92 " pdb=" N GLU H 92 " pdb=" C GLU H 92 " pdb=" CB GLU H 92 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA ASN b 77 " pdb=" N ASN b 77 " pdb=" C ASN b 77 " pdb=" CB ASN b 77 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 ... (remaining 755 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 81 " 0.120 5.00e-02 4.00e+02 1.80e-01 5.16e+01 pdb=" N PRO B 82 " -0.310 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.116 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 81 " -0.106 5.00e-02 4.00e+02 1.60e-01 4.08e+01 pdb=" N PRO A 82 " 0.276 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP b 81 " 0.108 5.00e-02 4.00e+02 1.40e-01 3.16e+01 pdb=" N PRO b 82 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO b 82 " 0.104 5.00e-02 4.00e+02 pdb=" CD PRO b 82 " 0.025 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 6 1.93 - 2.67: 385 2.67 - 3.42: 6307 3.42 - 4.16: 10163 4.16 - 4.90: 17330 Nonbonded interactions: 34191 Sorted by model distance: nonbonded pdb=" OE2 GLU B 104 " pdb=" NH2 ARG A 86 " model vdw 1.189 3.120 nonbonded pdb=" CZ2 TRP L 97 " pdb=" OG SER b 79 " model vdw 1.366 3.340 nonbonded pdb=" OD2 ASP B 126 " pdb=" NH2 ARG A 109 " model vdw 1.531 3.120 nonbonded pdb=" CD GLU B 104 " pdb=" NH2 ARG A 86 " model vdw 1.697 3.350 nonbonded pdb=" CE2 TRP L 97 " pdb=" OG SER b 79 " model vdw 1.865 3.260 ... (remaining 34186 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 'B' and resid 2 through 131) selection = (chain 'b' and resid 2 through 131) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.160 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.016 0.094 4778 Z= 1.069 Angle : 1.884 43.032 6500 Z= 1.121 Chirality : 0.110 0.861 758 Planarity : 0.014 0.180 848 Dihedral : 15.015 85.325 1751 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 1.64 % Allowed : 6.72 % Favored : 91.64 % Rotamer: Outliers : 11.15 % Allowed : 11.35 % Favored : 77.50 % Cbeta Deviations : 2.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.30), residues: 610 helix: -0.90 (0.54), residues: 70 sheet: -2.45 (0.28), residues: 263 loop : -2.67 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP L 97 HIS 0.003 0.001 HIS L 37 PHE 0.023 0.004 PHE L 74 TYR 0.040 0.003 TYR H 113 ARG 0.007 0.001 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.22654 ( 143) hydrogen bonds : angle 9.68809 ( 375) covalent geometry : bond 0.01570 ( 4778) covalent geometry : angle 1.88380 ( 6500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7894 (ptt90) cc_final: 0.5520 (mtt-85) REVERT: H 117 TYR cc_start: 0.8467 (m-80) cc_final: 0.8210 (m-10) REVERT: L 50 LEU cc_start: 0.9148 (mt) cc_final: 0.8788 (mp) REVERT: L 70 SER cc_start: 0.8934 (t) cc_final: 0.8552 (p) REVERT: L 92 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8453 (tm-30) REVERT: L 106 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8687 (mmmm) REVERT: b 37 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8620 (tm-30) REVERT: b 46 LYS cc_start: 0.8428 (mttp) cc_final: 0.8095 (mttm) REVERT: b 63 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8014 (ttmt) REVERT: b 123 ASP cc_start: 0.8592 (t0) cc_final: 0.8302 (t0) REVERT: b 129 ASN cc_start: 0.8875 (m110) cc_final: 0.8666 (m-40) REVERT: B 16 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8282 (mmtm) REVERT: B 24 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7649 (tpt170) REVERT: B 46 LYS cc_start: 0.8387 (mttp) cc_final: 0.8166 (mttm) REVERT: B 98 GLN cc_start: 0.8692 (tt0) cc_final: 0.8363 (tp40) REVERT: B 129 ASN cc_start: 0.9337 (m110) cc_final: 0.8925 (m110) REVERT: A 22 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8045 (p0) REVERT: A 30 ASN cc_start: 0.8035 (p0) cc_final: 0.7343 (p0) REVERT: A 32 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8279 (m) REVERT: A 34 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8665 (t) REVERT: A 53 SER cc_start: 0.9358 (m) cc_final: 0.8978 (p) REVERT: A 54 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: A 57 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7070 (ptt180) REVERT: A 63 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8893 (tttp) REVERT: A 65 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: A 68 ILE cc_start: 0.8973 (mt) cc_final: 0.8752 (mt) REVERT: A 72 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (p) REVERT: A 98 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8568 (pp30) REVERT: A 103 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8651 (mt-10) outliers start: 58 outliers final: 30 residues processed: 246 average time/residue: 0.2167 time to fit residues: 63.2137 Evaluate side-chains 182 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 80 CYS Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 128 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 129 ASN A 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070328 restraints weight = 10902.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.073168 restraints weight = 5113.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.075146 restraints weight = 3229.268| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 4778 Z= 0.284 Angle : 0.881 16.457 6500 Z= 0.447 Chirality : 0.053 0.260 758 Planarity : 0.011 0.174 848 Dihedral : 12.547 98.639 752 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.54 % Favored : 91.64 % Rotamer: Outliers : 9.04 % Allowed : 20.19 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.31), residues: 610 helix: -0.32 (0.58), residues: 75 sheet: -2.12 (0.32), residues: 233 loop : -2.42 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 97 HIS 0.004 0.001 HIS L 37 PHE 0.018 0.003 PHE b 107 TYR 0.028 0.002 TYR H 113 ARG 0.008 0.001 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 143) hydrogen bonds : angle 6.69309 ( 375) covalent geometry : bond 0.00655 ( 4778) covalent geometry : angle 0.88073 ( 6500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7475 (ptt90) cc_final: 0.4943 (mtt-85) REVERT: H 92 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8705 (mm-30) REVERT: H 101 ARG cc_start: 0.7653 (tpm170) cc_final: 0.7360 (mmm-85) REVERT: H 116 ASP cc_start: 0.8750 (p0) cc_final: 0.8125 (p0) REVERT: L 20 GLU cc_start: 0.8175 (mp0) cc_final: 0.7811 (pm20) REVERT: L 52 LYS cc_start: 0.8498 (tttt) cc_final: 0.8283 (ptmt) REVERT: L 92 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7446 (tm-30) REVERT: L 93 GLN cc_start: 0.8922 (pp30) cc_final: 0.7728 (pp30) REVERT: L 106 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8522 (mmmm) REVERT: b 37 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8450 (tm-30) REVERT: b 87 GLN cc_start: 0.8617 (mm110) cc_final: 0.8357 (mm110) REVERT: b 123 ASP cc_start: 0.8773 (t0) cc_final: 0.8482 (t0) REVERT: b 128 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8626 (mm) REVERT: b 129 ASN cc_start: 0.8640 (m110) cc_final: 0.8238 (m-40) REVERT: B 24 ARG cc_start: 0.8733 (mtp-110) cc_final: 0.7729 (tpt170) REVERT: B 69 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: B 104 GLU cc_start: 0.8371 (pt0) cc_final: 0.8080 (pt0) REVERT: B 127 GLN cc_start: 0.8394 (mp10) cc_final: 0.7766 (mp10) REVERT: A 34 SER cc_start: 0.8531 (m) cc_final: 0.8298 (t) REVERT: A 37 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 54 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: A 57 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6961 (ptt180) REVERT: A 69 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: A 77 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7958 (m-40) REVERT: A 102 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7645 (t70) REVERT: A 103 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8832 (mt-10) outliers start: 47 outliers final: 28 residues processed: 192 average time/residue: 0.1929 time to fit residues: 45.0433 Evaluate side-chains 176 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 80 CYS Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 122 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 70 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.070099 restraints weight = 10842.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.072740 restraints weight = 5751.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074564 restraints weight = 3885.568| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 4778 Z= 0.318 Angle : 0.867 13.726 6500 Z= 0.442 Chirality : 0.052 0.247 758 Planarity : 0.010 0.161 848 Dihedral : 10.820 83.966 715 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.51 % Favored : 89.84 % Rotamer: Outliers : 9.04 % Allowed : 21.15 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.32), residues: 610 helix: -0.04 (0.57), residues: 75 sheet: -2.05 (0.32), residues: 234 loop : -2.38 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 97 HIS 0.001 0.000 HIS H 63 PHE 0.018 0.003 PHE L 74 TYR 0.030 0.002 TYR H 113 ARG 0.005 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 143) hydrogen bonds : angle 6.39660 ( 375) covalent geometry : bond 0.00717 ( 4778) covalent geometry : angle 0.86693 ( 6500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7950 (ptt90) cc_final: 0.5233 (mtt-85) REVERT: H 92 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8398 (mm-30) REVERT: L 20 GLU cc_start: 0.8099 (mp0) cc_final: 0.7892 (pm20) REVERT: L 41 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8636 (tp40) REVERT: L 92 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8012 (tm-30) REVERT: L 106 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8614 (mmmm) REVERT: L 107 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9299 (tt) REVERT: b 14 ASP cc_start: 0.8308 (p0) cc_final: 0.7882 (p0) REVERT: b 37 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8570 (tm-30) REVERT: b 46 LYS cc_start: 0.8637 (mttm) cc_final: 0.8175 (mttm) REVERT: b 67 LYS cc_start: 0.8361 (mptt) cc_final: 0.7892 (mptt) REVERT: b 121 LEU cc_start: 0.9360 (tp) cc_final: 0.8975 (tp) REVERT: b 122 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8142 (tp) REVERT: b 123 ASP cc_start: 0.8865 (t0) cc_final: 0.8591 (t0) REVERT: b 128 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8849 (mm) REVERT: b 129 ASN cc_start: 0.8864 (m110) cc_final: 0.8449 (m110) REVERT: B 24 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.8020 (tpt170) REVERT: B 104 GLU cc_start: 0.8428 (pt0) cc_final: 0.8212 (pt0) REVERT: B 116 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9216 (tt) REVERT: B 127 GLN cc_start: 0.8561 (mp10) cc_final: 0.7791 (mp10) REVERT: A 34 SER cc_start: 0.8718 (m) cc_final: 0.8457 (t) REVERT: A 37 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8500 (tm-30) REVERT: A 47 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7920 (ptp90) REVERT: A 54 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: A 102 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7440 (t70) REVERT: A 103 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8462 (mt-10) outliers start: 47 outliers final: 33 residues processed: 176 average time/residue: 0.1984 time to fit residues: 42.2777 Evaluate side-chains 176 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 122 ILE Chi-restraints excluded: chain b residue 125 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 122 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.072304 restraints weight = 10870.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075071 restraints weight = 5592.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076953 restraints weight = 3724.648| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 4778 Z= 0.204 Angle : 0.772 11.615 6500 Z= 0.393 Chirality : 0.050 0.241 758 Planarity : 0.009 0.152 848 Dihedral : 9.800 86.385 709 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.39 % Favored : 92.95 % Rotamer: Outliers : 8.27 % Allowed : 24.62 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.32), residues: 610 helix: 0.29 (0.58), residues: 76 sheet: -1.84 (0.32), residues: 236 loop : -2.41 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 50 HIS 0.002 0.001 HIS L 37 PHE 0.013 0.002 PHE A 96 TYR 0.023 0.002 TYR H 113 ARG 0.005 0.001 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 143) hydrogen bonds : angle 5.88051 ( 375) covalent geometry : bond 0.00485 ( 4778) covalent geometry : angle 0.77182 ( 6500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.585 Fit side-chains REVERT: H 47 ARG cc_start: 0.7813 (ptt90) cc_final: 0.5241 (mtt-85) REVERT: H 92 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8472 (mm-30) REVERT: L 92 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8096 (tm-30) REVERT: L 106 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8512 (mmmm) REVERT: b 14 ASP cc_start: 0.8596 (p0) cc_final: 0.8075 (p0) REVERT: b 16 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8817 (mmmm) REVERT: b 37 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8642 (tm-30) REVERT: b 67 LYS cc_start: 0.8304 (mptt) cc_final: 0.7849 (mptt) REVERT: b 123 ASP cc_start: 0.8798 (t0) cc_final: 0.8554 (t0) REVERT: b 128 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8873 (mm) REVERT: b 129 ASN cc_start: 0.8833 (m110) cc_final: 0.8403 (m110) REVERT: B 24 ARG cc_start: 0.8752 (mtp-110) cc_final: 0.7896 (tpt170) REVERT: B 98 GLN cc_start: 0.8766 (tt0) cc_final: 0.8534 (tp40) REVERT: B 116 LEU cc_start: 0.9478 (mt) cc_final: 0.9206 (tt) REVERT: B 127 GLN cc_start: 0.8616 (mp10) cc_final: 0.8170 (mp10) REVERT: A 6 VAL cc_start: 0.7991 (t) cc_final: 0.7635 (m) REVERT: A 34 SER cc_start: 0.8606 (m) cc_final: 0.8280 (t) REVERT: A 37 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 54 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: A 69 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7408 (tm130) REVERT: A 103 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8579 (mt-10) outliers start: 43 outliers final: 28 residues processed: 172 average time/residue: 0.1959 time to fit residues: 41.0943 Evaluate side-chains 166 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 80 CYS Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 0.0050 chunk 37 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 87 GLN B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070409 restraints weight = 10970.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.073225 restraints weight = 5338.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075151 restraints weight = 3416.196| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 4778 Z= 0.197 Angle : 0.757 10.323 6500 Z= 0.385 Chirality : 0.049 0.229 758 Planarity : 0.009 0.145 848 Dihedral : 8.910 87.980 699 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.54 % Favored : 91.80 % Rotamer: Outliers : 8.65 % Allowed : 24.42 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.32), residues: 610 helix: 0.41 (0.58), residues: 76 sheet: -1.76 (0.32), residues: 242 loop : -2.33 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 50 HIS 0.003 0.001 HIS L 37 PHE 0.010 0.002 PHE b 107 TYR 0.021 0.001 TYR H 113 ARG 0.002 0.000 ARG b 24 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 143) hydrogen bonds : angle 5.58962 ( 375) covalent geometry : bond 0.00473 ( 4778) covalent geometry : angle 0.75662 ( 6500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7257 (ptt90) cc_final: 0.4956 (mtt-85) REVERT: H 92 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8674 (mm-30) REVERT: H 116 ASP cc_start: 0.8756 (p0) cc_final: 0.8554 (p0) REVERT: L 40 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: L 92 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7767 (tm-30) REVERT: L 96 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8606 (mmm-85) REVERT: L 105 THR cc_start: 0.8088 (m) cc_final: 0.7744 (m) REVERT: L 106 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8426 (mmmm) REVERT: L 107 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9144 (tt) REVERT: b 14 ASP cc_start: 0.8688 (p0) cc_final: 0.7913 (p0) REVERT: b 16 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8808 (mmmm) REVERT: b 37 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8413 (tm-30) REVERT: b 67 LYS cc_start: 0.7861 (mptt) cc_final: 0.7365 (mptt) REVERT: b 123 ASP cc_start: 0.8677 (t0) cc_final: 0.8409 (t0) REVERT: b 129 ASN cc_start: 0.8603 (m110) cc_final: 0.8068 (m110) REVERT: B 24 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.7562 (tpt170) REVERT: B 98 GLN cc_start: 0.9045 (tt0) cc_final: 0.8588 (tp40) REVERT: B 127 GLN cc_start: 0.8771 (mp10) cc_final: 0.8062 (mp10) REVERT: A 6 VAL cc_start: 0.7998 (t) cc_final: 0.7625 (m) REVERT: A 34 SER cc_start: 0.8552 (m) cc_final: 0.8111 (t) REVERT: A 37 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 54 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: A 102 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7786 (t70) REVERT: A 103 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8708 (mt-10) REVERT: A 129 ASN cc_start: 0.8440 (m-40) cc_final: 0.8201 (m-40) outliers start: 45 outliers final: 30 residues processed: 177 average time/residue: 0.1871 time to fit residues: 40.4525 Evaluate side-chains 178 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 80 CYS Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 125 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN b 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.071227 restraints weight = 10741.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.074062 restraints weight = 5221.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076021 restraints weight = 3356.677| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 4778 Z= 0.164 Angle : 0.753 9.306 6500 Z= 0.380 Chirality : 0.048 0.222 758 Planarity : 0.009 0.140 848 Dihedral : 7.737 54.999 696 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.90 % Favored : 93.44 % Rotamer: Outliers : 7.50 % Allowed : 25.96 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.33), residues: 610 helix: 0.59 (0.58), residues: 76 sheet: -1.51 (0.33), residues: 241 loop : -2.24 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.003 0.002 HIS L 37 PHE 0.011 0.002 PHE A 96 TYR 0.016 0.001 TYR H 113 ARG 0.003 0.000 ARG b 86 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 143) hydrogen bonds : angle 5.32453 ( 375) covalent geometry : bond 0.00407 ( 4778) covalent geometry : angle 0.75305 ( 6500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7179 (ptt90) cc_final: 0.4874 (mtt-85) REVERT: H 68 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8332 (mmmt) REVERT: H 92 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8637 (mm-30) REVERT: L 40 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: L 92 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7775 (tm-30) REVERT: L 105 THR cc_start: 0.8055 (m) cc_final: 0.7656 (m) REVERT: L 106 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8398 (mmmm) REVERT: b 10 ASN cc_start: 0.9175 (m-40) cc_final: 0.8801 (p0) REVERT: b 14 ASP cc_start: 0.8677 (p0) cc_final: 0.7929 (p0) REVERT: b 16 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8798 (mmmm) REVERT: b 37 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8557 (tm-30) REVERT: b 67 LYS cc_start: 0.7775 (mptt) cc_final: 0.7310 (mptt) REVERT: b 123 ASP cc_start: 0.8633 (t0) cc_final: 0.8388 (t0) REVERT: b 129 ASN cc_start: 0.8624 (m110) cc_final: 0.8093 (m110) REVERT: B 10 ASN cc_start: 0.8870 (p0) cc_final: 0.8596 (p0) REVERT: B 24 ARG cc_start: 0.8804 (mtp-110) cc_final: 0.7569 (tpt170) REVERT: B 98 GLN cc_start: 0.9056 (tt0) cc_final: 0.8652 (tp40) REVERT: B 116 LEU cc_start: 0.9358 (mt) cc_final: 0.9154 (tt) REVERT: B 127 GLN cc_start: 0.8770 (mp10) cc_final: 0.8065 (mp10) REVERT: B 129 ASN cc_start: 0.9201 (m-40) cc_final: 0.8894 (m-40) REVERT: A 6 VAL cc_start: 0.7975 (t) cc_final: 0.7612 (m) REVERT: A 34 SER cc_start: 0.8506 (m) cc_final: 0.8065 (t) REVERT: A 37 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 69 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6702 (tm130) REVERT: A 103 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8702 (mt-10) REVERT: A 127 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8682 (mm110) REVERT: A 129 ASN cc_start: 0.8404 (m-40) cc_final: 0.8149 (m-40) outliers start: 39 outliers final: 30 residues processed: 177 average time/residue: 0.1888 time to fit residues: 40.7457 Evaluate side-chains 178 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.071878 restraints weight = 10702.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074758 restraints weight = 5160.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076741 restraints weight = 3282.711| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 4778 Z= 0.143 Angle : 0.738 8.249 6500 Z= 0.373 Chirality : 0.048 0.215 758 Planarity : 0.008 0.135 848 Dihedral : 7.139 53.362 692 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.57 % Favored : 93.77 % Rotamer: Outliers : 6.92 % Allowed : 26.54 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.33), residues: 610 helix: 0.69 (0.58), residues: 76 sheet: -1.21 (0.34), residues: 237 loop : -2.22 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 50 HIS 0.003 0.002 HIS L 37 PHE 0.018 0.002 PHE H 30 TYR 0.013 0.001 TYR H 113 ARG 0.006 0.000 ARG b 24 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 143) hydrogen bonds : angle 5.09787 ( 375) covalent geometry : bond 0.00371 ( 4778) covalent geometry : angle 0.73821 ( 6500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7822 (tp40) REVERT: H 47 ARG cc_start: 0.7054 (ptt90) cc_final: 0.4691 (mtt-85) REVERT: H 68 LYS cc_start: 0.8557 (mmmm) cc_final: 0.8343 (mmmt) REVERT: H 85 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7637 (tp-100) REVERT: H 92 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8542 (mm-30) REVERT: L 40 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: L 92 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7760 (tm-30) REVERT: L 105 THR cc_start: 0.8022 (m) cc_final: 0.7592 (m) REVERT: L 106 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8354 (mmmm) REVERT: b 10 ASN cc_start: 0.9125 (m-40) cc_final: 0.8780 (p0) REVERT: b 14 ASP cc_start: 0.8723 (p0) cc_final: 0.8038 (p0) REVERT: b 16 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8814 (mmmm) REVERT: b 37 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8299 (tm-30) REVERT: b 67 LYS cc_start: 0.7610 (mptt) cc_final: 0.7143 (mptt) REVERT: b 123 ASP cc_start: 0.8655 (t0) cc_final: 0.8390 (t0) REVERT: b 129 ASN cc_start: 0.8602 (m110) cc_final: 0.8100 (m110) REVERT: B 24 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.7535 (tpt170) REVERT: B 59 ARG cc_start: 0.8070 (ptt180) cc_final: 0.7831 (ptt180) REVERT: B 98 GLN cc_start: 0.9014 (tt0) cc_final: 0.8678 (tp40) REVERT: B 127 GLN cc_start: 0.8765 (mp10) cc_final: 0.8046 (mp10) REVERT: B 128 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8502 (mm) REVERT: B 129 ASN cc_start: 0.9200 (m-40) cc_final: 0.8854 (m-40) REVERT: A 6 VAL cc_start: 0.7873 (t) cc_final: 0.7521 (m) REVERT: A 34 SER cc_start: 0.8601 (m) cc_final: 0.8167 (t) REVERT: A 37 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 68 ILE cc_start: 0.8285 (mt) cc_final: 0.8079 (mp) REVERT: A 103 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8663 (mt-10) REVERT: A 127 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8606 (mm110) REVERT: A 129 ASN cc_start: 0.8473 (m-40) cc_final: 0.8192 (m-40) outliers start: 36 outliers final: 23 residues processed: 178 average time/residue: 0.2049 time to fit residues: 44.7461 Evaluate side-chains 174 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 22 optimal weight: 0.0050 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.072131 restraints weight = 10678.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075015 restraints weight = 5089.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077002 restraints weight = 3244.688| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 4778 Z= 0.142 Angle : 0.741 10.435 6500 Z= 0.371 Chirality : 0.048 0.214 758 Planarity : 0.008 0.131 848 Dihedral : 6.677 49.695 690 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.57 % Favored : 93.77 % Rotamer: Outliers : 6.15 % Allowed : 26.35 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.33), residues: 610 helix: 0.48 (0.56), residues: 77 sheet: -1.06 (0.34), residues: 237 loop : -2.13 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 50 HIS 0.002 0.002 HIS L 37 PHE 0.010 0.001 PHE B 94 TYR 0.012 0.001 TYR H 105 ARG 0.003 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 143) hydrogen bonds : angle 4.99105 ( 375) covalent geometry : bond 0.00367 ( 4778) covalent geometry : angle 0.74127 ( 6500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7035 (ptt90) cc_final: 0.4758 (mtt-85) REVERT: H 68 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8269 (mmmt) REVERT: H 85 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7651 (tp-100) REVERT: H 92 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8723 (mm-30) REVERT: H 105 TYR cc_start: 0.8774 (p90) cc_final: 0.8400 (p90) REVERT: L 40 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: L 92 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7678 (tm-30) REVERT: L 105 THR cc_start: 0.8049 (m) cc_final: 0.7732 (m) REVERT: L 106 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8282 (mmmm) REVERT: b 10 ASN cc_start: 0.9140 (m-40) cc_final: 0.8811 (p0) REVERT: b 14 ASP cc_start: 0.8702 (p0) cc_final: 0.8028 (p0) REVERT: b 16 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8777 (mmmm) REVERT: b 37 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8289 (tm-30) REVERT: b 67 LYS cc_start: 0.7563 (mptt) cc_final: 0.7128 (mptt) REVERT: b 123 ASP cc_start: 0.8616 (t0) cc_final: 0.8378 (t0) REVERT: b 129 ASN cc_start: 0.8619 (m110) cc_final: 0.8155 (m110) REVERT: B 24 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.7509 (tpt170) REVERT: B 59 ARG cc_start: 0.8085 (ptt180) cc_final: 0.7833 (ptt180) REVERT: B 98 GLN cc_start: 0.9013 (tt0) cc_final: 0.8691 (tp40) REVERT: B 127 GLN cc_start: 0.8688 (mp10) cc_final: 0.7994 (mp10) REVERT: B 128 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 6 VAL cc_start: 0.7903 (t) cc_final: 0.7525 (m) REVERT: A 34 SER cc_start: 0.8562 (m) cc_final: 0.8136 (t) REVERT: A 37 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8640 (tm-30) REVERT: A 69 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6458 (tm130) REVERT: A 103 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8719 (mt-10) REVERT: A 121 LEU cc_start: 0.9185 (tp) cc_final: 0.8904 (tt) REVERT: A 127 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8680 (mm110) REVERT: A 129 ASN cc_start: 0.8453 (m-40) cc_final: 0.8165 (m-40) outliers start: 32 outliers final: 24 residues processed: 171 average time/residue: 0.1893 time to fit residues: 39.6754 Evaluate side-chains 175 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 56 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.4520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN A 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.072778 restraints weight = 10749.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.075716 restraints weight = 5074.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077738 restraints weight = 3209.793| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 4778 Z= 0.144 Angle : 0.753 9.570 6500 Z= 0.376 Chirality : 0.048 0.201 758 Planarity : 0.008 0.128 848 Dihedral : 6.546 48.816 688 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.08 % Favored : 94.43 % Rotamer: Outliers : 5.96 % Allowed : 27.88 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.33), residues: 610 helix: 0.64 (0.56), residues: 77 sheet: -0.94 (0.34), residues: 235 loop : -2.06 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 39 HIS 0.003 0.002 HIS H 63 PHE 0.010 0.001 PHE B 94 TYR 0.020 0.001 TYR H 105 ARG 0.004 0.000 ARG L 96 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 143) hydrogen bonds : angle 4.88092 ( 375) covalent geometry : bond 0.00373 ( 4778) covalent geometry : angle 0.75340 ( 6500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7074 (ptt90) cc_final: 0.4786 (mtt-85) REVERT: H 68 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8283 (mmmt) REVERT: H 85 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7404 (tp-100) REVERT: H 92 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8719 (mm-30) REVERT: L 40 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: L 92 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7672 (tm-30) REVERT: L 105 THR cc_start: 0.7940 (m) cc_final: 0.7393 (m) REVERT: L 106 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8253 (mmmm) REVERT: L 107 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9198 (tt) REVERT: b 10 ASN cc_start: 0.9157 (m-40) cc_final: 0.8848 (p0) REVERT: b 14 ASP cc_start: 0.8656 (p0) cc_final: 0.8043 (p0) REVERT: b 16 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8866 (mmmm) REVERT: b 37 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8366 (tm-30) REVERT: b 67 LYS cc_start: 0.7594 (mptt) cc_final: 0.7121 (mptt) REVERT: b 123 ASP cc_start: 0.8575 (t0) cc_final: 0.8361 (t0) REVERT: b 129 ASN cc_start: 0.8656 (m110) cc_final: 0.8230 (m110) REVERT: B 10 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8548 (p0) REVERT: B 24 ARG cc_start: 0.8695 (mtp-110) cc_final: 0.7357 (tpt170) REVERT: B 37 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7910 (tp40) REVERT: B 59 ARG cc_start: 0.8194 (ptt180) cc_final: 0.7916 (ptt180) REVERT: B 98 GLN cc_start: 0.9014 (tt0) cc_final: 0.8692 (tp40) REVERT: B 127 GLN cc_start: 0.8687 (mp10) cc_final: 0.8077 (mp10) REVERT: B 128 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8436 (mm) REVERT: B 129 ASN cc_start: 0.8962 (m110) cc_final: 0.8730 (m-40) REVERT: A 10 ASN cc_start: 0.9143 (t0) cc_final: 0.8854 (p0) REVERT: A 34 SER cc_start: 0.8569 (m) cc_final: 0.8138 (t) REVERT: A 37 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8598 (tm-30) REVERT: A 69 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6420 (tm130) REVERT: A 102 ASP cc_start: 0.8276 (t70) cc_final: 0.7821 (t0) REVERT: A 103 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8703 (mt-10) REVERT: A 121 LEU cc_start: 0.9160 (tp) cc_final: 0.8871 (tp) REVERT: A 127 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8795 (mm-40) REVERT: A 129 ASN cc_start: 0.8450 (m-40) cc_final: 0.8155 (m-40) outliers start: 31 outliers final: 22 residues processed: 169 average time/residue: 0.1944 time to fit residues: 40.0991 Evaluate side-chains 175 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.072763 restraints weight = 10754.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075704 restraints weight = 5124.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077741 restraints weight = 3252.200| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 4778 Z= 0.280 Angle : 1.193 59.157 6500 Z= 0.687 Chirality : 0.050 0.301 758 Planarity : 0.008 0.127 848 Dihedral : 6.602 48.690 688 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.90 % Favored : 93.61 % Rotamer: Outliers : 5.58 % Allowed : 28.85 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.33), residues: 610 helix: 0.65 (0.56), residues: 77 sheet: -0.96 (0.34), residues: 235 loop : -2.09 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS H 63 PHE 0.011 0.002 PHE A 96 TYR 0.021 0.002 TYR H 110 ARG 0.003 0.000 ARG b 24 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 143) hydrogen bonds : angle 4.87297 ( 375) covalent geometry : bond 0.00604 ( 4778) covalent geometry : angle 1.19295 ( 6500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 ARG cc_start: 0.7087 (ptt90) cc_final: 0.4798 (mtt-85) REVERT: H 68 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8284 (mmmt) REVERT: H 85 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7401 (tp-100) REVERT: H 92 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8728 (mm-30) REVERT: L 40 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: L 92 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7693 (tm-30) REVERT: L 105 THR cc_start: 0.7982 (m) cc_final: 0.7430 (m) REVERT: L 106 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8269 (mmmm) REVERT: L 107 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9211 (tt) REVERT: b 10 ASN cc_start: 0.9158 (m-40) cc_final: 0.8851 (p0) REVERT: b 14 ASP cc_start: 0.8656 (p0) cc_final: 0.8045 (p0) REVERT: b 16 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8870 (mmmm) REVERT: b 37 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8393 (tm-30) REVERT: b 67 LYS cc_start: 0.7611 (mptt) cc_final: 0.7159 (mptt) REVERT: b 123 ASP cc_start: 0.8585 (t0) cc_final: 0.8370 (t0) REVERT: b 129 ASN cc_start: 0.8669 (m110) cc_final: 0.8244 (m110) REVERT: B 24 ARG cc_start: 0.8683 (mtp-110) cc_final: 0.7366 (tpt170) REVERT: B 37 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8075 (tp40) REVERT: B 45 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6655 (mt-10) REVERT: B 59 ARG cc_start: 0.8165 (ptt180) cc_final: 0.7925 (ptt180) REVERT: B 98 GLN cc_start: 0.9014 (tt0) cc_final: 0.8706 (tp40) REVERT: B 127 GLN cc_start: 0.8702 (mp10) cc_final: 0.8080 (mp10) REVERT: B 128 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 10 ASN cc_start: 0.9149 (t0) cc_final: 0.8859 (p0) REVERT: A 34 SER cc_start: 0.8574 (m) cc_final: 0.8144 (t) REVERT: A 37 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8605 (tm-30) REVERT: A 69 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6456 (tm130) REVERT: A 102 ASP cc_start: 0.8306 (t70) cc_final: 0.7839 (t0) REVERT: A 103 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8710 (mt-10) REVERT: A 121 LEU cc_start: 0.9165 (tp) cc_final: 0.8879 (tp) REVERT: A 127 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8798 (mm-40) REVERT: A 129 ASN cc_start: 0.8461 (m-40) cc_final: 0.8166 (m-40) outliers start: 29 outliers final: 25 residues processed: 165 average time/residue: 0.2076 time to fit residues: 41.8333 Evaluate side-chains 176 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 113 TYR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 87 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.072605 restraints weight = 10872.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075573 restraints weight = 5153.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077612 restraints weight = 3257.977| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 4778 Z= 0.280 Angle : 1.193 59.156 6500 Z= 0.687 Chirality : 0.050 0.301 758 Planarity : 0.008 0.127 848 Dihedral : 6.602 48.690 688 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.90 % Favored : 93.61 % Rotamer: Outliers : 5.58 % Allowed : 29.23 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.33), residues: 610 helix: 0.65 (0.56), residues: 77 sheet: -0.96 (0.34), residues: 235 loop : -2.09 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS H 63 PHE 0.011 0.002 PHE A 96 TYR 0.021 0.002 TYR H 110 ARG 0.003 0.000 ARG b 24 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 143) hydrogen bonds : angle 4.87297 ( 375) covalent geometry : bond 0.00604 ( 4778) covalent geometry : angle 1.19294 ( 6500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.35 seconds wall clock time: 35 minutes 4.16 seconds (2104.16 seconds total)