Starting phenix.real_space_refine on Fri Feb 14 12:24:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcd_36158/02_2025/8jcd_36158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcd_36158/02_2025/8jcd_36158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcd_36158/02_2025/8jcd_36158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcd_36158/02_2025/8jcd_36158.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcd_36158/02_2025/8jcd_36158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcd_36158/02_2025/8jcd_36158.cif" } resolution = 3.14 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= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 240 5.49 5 S 16 5.16 5 C 5838 2.51 5 N 1986 2.21 5 O 2426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10506 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "E" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 752 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "H" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "I" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2476 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Chain: "J" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2444 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Time building chain proxies: 6.04, per 1000 atoms: 0.57 Number of scatterers: 10506 At special positions: 0 Unit cell: (81.62, 114.48, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 240 15.00 O 2426 8.00 N 1986 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 683.3 milliseconds 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 75.7% alpha, 2.8% beta 119 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.610A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.545A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.707A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.667A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 59 through 69 removed outlier: 4.013A pdb=" N ARG D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 106 removed outlier: 3.885A pdb=" N SER D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 124 through 149 removed outlier: 3.521A pdb=" N LYS D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN D 149 " --> pdb=" O TYR D 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.692A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.643A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.270A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.696A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 76 through 105 Processing helix chain 'H' and resid 111 through 123 Processing helix chain 'H' and resid 125 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.994A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.645A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.255A pdb=" N ARG C 42 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.749A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.906A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.623A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 384 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 119 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2044 1.33 - 1.45: 3571 1.45 - 1.57: 5047 1.57 - 1.69: 478 1.69 - 1.81: 28 Bond restraints: 11168 Sorted by residual: bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 1.532 1.552 -0.020 1.74e-02 3.30e+03 1.36e+00 bond pdb=" CB MET H 83 " pdb=" CG MET H 83 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" C3' DG J -7 " pdb=" C2' DG J -7 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.46e-01 ... (remaining 11163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 15902 2.16 - 4.31: 188 4.31 - 6.47: 8 6.47 - 8.62: 2 8.62 - 10.78: 2 Bond angle restraints: 16102 Sorted by residual: angle pdb=" CB MET H 83 " pdb=" CG MET H 83 " pdb=" SD MET H 83 " ideal model delta sigma weight residual 112.70 101.92 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C GLU C 61 " pdb=" N ILE C 62 " pdb=" CA ILE C 62 " ideal model delta sigma weight residual 121.97 127.52 -5.55 1.80e+00 3.09e-01 9.51e+00 angle pdb=" CA LEU H 121 " pdb=" CB LEU H 121 " pdb=" CG LEU H 121 " ideal model delta sigma weight residual 116.30 125.06 -8.76 3.50e+00 8.16e-02 6.26e+00 angle pdb=" CB GLN F 27 " pdb=" CG GLN F 27 " pdb=" CD GLN F 27 " ideal model delta sigma weight residual 112.60 116.28 -3.68 1.70e+00 3.46e-01 4.69e+00 angle pdb=" CA LEU D 140 " pdb=" CB LEU D 140 " pdb=" CG LEU D 140 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.65e+00 ... (remaining 16097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 4847 35.77 - 71.55: 1221 71.55 - 107.32: 12 107.32 - 143.10: 1 143.10 - 178.87: 1 Dihedral angle restraints: 6082 sinusoidal: 4056 harmonic: 2026 Sorted by residual: dihedral pdb=" CA ALA C 60 " pdb=" C ALA C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.87 -178.87 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.26 131.74 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 6079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1538 0.045 - 0.090: 260 0.090 - 0.135: 40 0.135 - 0.180: 2 0.180 - 0.225: 2 Chirality restraints: 1842 Sorted by residual: chirality pdb=" CG LEU G 63 " pdb=" CB LEU G 63 " pdb=" CD1 LEU G 63 " pdb=" CD2 LEU G 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU H 121 " pdb=" CB LEU H 121 " pdb=" CD1 LEU H 121 " pdb=" CD2 LEU H 121 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1839 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " 0.023 2.00e-02 2.50e+03 1.01e-02 2.83e+00 pdb=" N9 DA I 26 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO C 80 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 61 " 0.009 2.00e-02 2.50e+03 1.08e-02 2.34e+00 pdb=" CG TYR D 61 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 61 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 61 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 61 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 61 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 61 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 61 " -0.001 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1121 2.75 - 3.29: 9702 3.29 - 3.82: 20983 3.82 - 4.36: 23281 4.36 - 4.90: 34800 Nonbonded interactions: 89887 Sorted by model distance: nonbonded pdb=" OD2 ASP D 89 " pdb=" OH TYR F 98 " model vdw 2.208 3.040 nonbonded pdb=" O ILE G 78 " pdb=" OG SER H 76 " model vdw 2.215 3.040 nonbonded pdb=" N2 DG I 18 " pdb=" O2 DT J -17 " model vdw 2.225 3.120 nonbonded pdb=" O LEU A 61 " pdb=" NH2 ARG B 36 " model vdw 2.232 3.120 nonbonded pdb=" NE2 HIS B 75 " pdb=" OE2 GLU D 114 " model vdw 2.259 3.120 ... (remaining 89882 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 'B' and resid 22 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 105) } ncs_group { reference = (chain 'D' and resid 57 through 146) selection = (chain 'H' and resid 57 through 146) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.090 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.003 0.038 11168 Z= 0.190 Angle : 0.574 10.776 16102 Z= 0.333 Chirality : 0.035 0.225 1842 Planarity : 0.004 0.042 1208 Dihedral : 28.678 178.870 4774 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 0.69 % Allowed : 35.68 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.32), residues: 688 helix: 1.93 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.014 0.001 PHE C 25 TYR 0.026 0.001 TYR D 61 ARG 0.009 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7753 (tm-30) REVERT: A 59 GLU cc_start: 0.8231 (pm20) cc_final: 0.7667 (pm20) REVERT: A 97 GLU cc_start: 0.8707 (tt0) cc_final: 0.8422 (tt0) REVERT: A 133 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8275 (tt0) REVERT: B 30 THR cc_start: 0.9113 (p) cc_final: 0.8760 (t) REVERT: B 98 TYR cc_start: 0.8755 (m-10) cc_final: 0.8487 (m-10) REVERT: C 56 GLU cc_start: 0.8844 (tt0) cc_final: 0.8495 (tt0) REVERT: C 68 ASN cc_start: 0.9424 (m-40) cc_final: 0.8403 (m-40) REVERT: C 95 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8557 (tppt) REVERT: D 78 GLU cc_start: 0.8730 (mp0) cc_final: 0.8484 (mp0) REVERT: E 133 GLU cc_start: 0.8565 (pt0) cc_final: 0.8327 (pt0) REVERT: F 25 ASN cc_start: 0.9195 (m-40) cc_final: 0.8526 (t0) REVERT: F 79 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7915 (mttt) REVERT: F 88 TYR cc_start: 0.9403 (m-80) cc_final: 0.9197 (m-80) REVERT: F 91 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8965 (ttmt) REVERT: G 81 ARG cc_start: 0.8639 (tpt170) cc_final: 0.8265 (tpt170) REVERT: G 95 LYS cc_start: 0.9339 (ttmt) cc_final: 0.9073 (ttmm) REVERT: G 104 GLN cc_start: 0.8635 (mp10) cc_final: 0.8267 (mp10) REVERT: H 85 SER cc_start: 0.9249 (t) cc_final: 0.8963 (t) REVERT: H 89 ASP cc_start: 0.9030 (t70) cc_final: 0.8599 (t0) REVERT: H 92 ASP cc_start: 0.9232 (t70) cc_final: 0.8998 (t0) REVERT: H 141 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8548 (ttm110) outliers start: 4 outliers final: 1 residues processed: 234 average time/residue: 0.3383 time to fit residues: 99.7673 Evaluate side-chains 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.083421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.056478 restraints weight = 30959.612| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.85 r_work: 0.2688 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11168 Z= 0.294 Angle : 0.600 7.715 16102 Z= 0.352 Chirality : 0.036 0.173 1842 Planarity : 0.004 0.041 1208 Dihedral : 30.550 178.835 3392 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 4.12 % Allowed : 34.82 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.23 (0.33), residues: 688 helix: 2.22 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -1.32 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.010 0.001 PHE C 25 TYR 0.019 0.002 TYR D 61 ARG 0.006 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7543 (tm-30) REVERT: A 59 GLU cc_start: 0.7993 (pm20) cc_final: 0.7603 (pm20) REVERT: A 133 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8426 (tt0) REVERT: B 84 MET cc_start: 0.8352 (tpp) cc_final: 0.8085 (tpp) REVERT: C 24 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8784 (mm110) REVERT: C 38 ASN cc_start: 0.8906 (t0) cc_final: 0.8519 (t0) REVERT: C 56 GLU cc_start: 0.8635 (tt0) cc_final: 0.8296 (tt0) REVERT: C 68 ASN cc_start: 0.8909 (m-40) cc_final: 0.8438 (m-40) REVERT: D 127 MET cc_start: 0.8468 (ttm) cc_final: 0.8265 (ttm) REVERT: E 73 GLU cc_start: 0.9032 (tt0) cc_final: 0.8831 (tt0) REVERT: E 94 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8636 (mm-30) REVERT: E 133 GLU cc_start: 0.8524 (pt0) cc_final: 0.8304 (pt0) REVERT: F 25 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8217 (t0) REVERT: F 50 ILE cc_start: 0.9233 (mm) cc_final: 0.9019 (mt) REVERT: F 84 MET cc_start: 0.8571 (tpp) cc_final: 0.8188 (tpp) REVERT: F 88 TYR cc_start: 0.9098 (m-80) cc_final: 0.8843 (m-80) REVERT: F 91 LYS cc_start: 0.9189 (ttpt) cc_final: 0.8969 (ttmt) REVERT: F 98 TYR cc_start: 0.9187 (m-10) cc_final: 0.8964 (m-80) REVERT: G 38 ASN cc_start: 0.9332 (t0) cc_final: 0.9117 (t0) REVERT: G 41 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9060 (mt-10) REVERT: G 81 ARG cc_start: 0.8602 (tpt170) cc_final: 0.8203 (tpt170) REVERT: G 95 LYS cc_start: 0.9347 (ttmt) cc_final: 0.9134 (ttmm) REVERT: G 104 GLN cc_start: 0.8702 (mp10) cc_final: 0.8363 (mp10) REVERT: H 77 ARG cc_start: 0.8600 (ttp-110) cc_final: 0.8244 (mtm-85) REVERT: H 85 SER cc_start: 0.8972 (t) cc_final: 0.8587 (t) REVERT: H 89 ASP cc_start: 0.8935 (t70) cc_final: 0.8647 (t0) REVERT: H 141 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8456 (ttm110) outliers start: 24 outliers final: 11 residues processed: 227 average time/residue: 0.3226 time to fit residues: 93.0174 Evaluate side-chains 205 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.083483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.057495 restraints weight = 31306.878| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.89 r_work: 0.2707 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11168 Z= 0.241 Angle : 0.587 8.418 16102 Z= 0.343 Chirality : 0.035 0.211 1842 Planarity : 0.004 0.044 1208 Dihedral : 30.599 178.472 3390 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.95 % Allowed : 35.16 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.38 (0.33), residues: 688 helix: 2.33 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.008 0.001 PHE C 25 TYR 0.019 0.002 TYR D 61 ARG 0.006 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7590 (tm-30) REVERT: A 59 GLU cc_start: 0.8106 (pm20) cc_final: 0.7679 (pm20) REVERT: A 94 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8854 (mm-30) REVERT: A 133 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8411 (tt0) REVERT: B 74 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8850 (mm-30) REVERT: B 84 MET cc_start: 0.8367 (tpp) cc_final: 0.8111 (tpp) REVERT: B 92 ARG cc_start: 0.9138 (ttp80) cc_final: 0.8665 (mmm-85) REVERT: C 24 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8753 (mm110) REVERT: C 38 ASN cc_start: 0.8900 (t0) cc_final: 0.8670 (t0) REVERT: C 56 GLU cc_start: 0.8618 (tt0) cc_final: 0.8220 (tt0) REVERT: C 68 ASN cc_start: 0.8849 (m-40) cc_final: 0.8566 (m-40) REVERT: D 137 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8403 (mtmm) REVERT: E 73 GLU cc_start: 0.9024 (tt0) cc_final: 0.8735 (tt0) REVERT: E 133 GLU cc_start: 0.8525 (pt0) cc_final: 0.8207 (pt0) REVERT: F 25 ASN cc_start: 0.9013 (m-40) cc_final: 0.8189 (t0) REVERT: F 84 MET cc_start: 0.8584 (tpp) cc_final: 0.8223 (tpp) REVERT: F 88 TYR cc_start: 0.9104 (m-80) cc_final: 0.8864 (m-80) REVERT: F 91 LYS cc_start: 0.9162 (ttpt) cc_final: 0.8928 (ttmt) REVERT: G 41 GLU cc_start: 0.9251 (mt-10) cc_final: 0.9009 (mt-10) REVERT: G 81 ARG cc_start: 0.8571 (tpt170) cc_final: 0.8224 (tpt170) REVERT: G 104 GLN cc_start: 0.8767 (mp10) cc_final: 0.8454 (mp10) REVERT: H 77 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8231 (mtm-85) REVERT: H 85 SER cc_start: 0.8885 (t) cc_final: 0.8679 (t) REVERT: H 141 ARG cc_start: 0.8913 (mtp85) cc_final: 0.8451 (ttm110) outliers start: 23 outliers final: 11 residues processed: 215 average time/residue: 0.3339 time to fit residues: 91.2886 Evaluate side-chains 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.082676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056244 restraints weight = 30900.423| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.90 r_work: 0.2689 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11168 Z= 0.262 Angle : 0.591 8.744 16102 Z= 0.346 Chirality : 0.035 0.245 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.728 178.160 3390 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 5.32 % Allowed : 34.13 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.33), residues: 688 helix: 2.36 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE E 104 TYR 0.020 0.001 TYR D 61 ARG 0.005 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7568 (tm-30) REVERT: A 59 GLU cc_start: 0.8174 (pm20) cc_final: 0.7764 (pm20) REVERT: A 94 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8727 (mm-30) REVERT: A 133 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8383 (tt0) REVERT: B 74 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8906 (mm-30) REVERT: B 84 MET cc_start: 0.8355 (tpp) cc_final: 0.8141 (tpp) REVERT: C 24 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8771 (mm110) REVERT: C 25 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.7484 (t80) REVERT: C 56 GLU cc_start: 0.8659 (tt0) cc_final: 0.8263 (tt0) REVERT: C 68 ASN cc_start: 0.8762 (m-40) cc_final: 0.8529 (m-40) REVERT: D 71 GLN cc_start: 0.8998 (pp30) cc_final: 0.8783 (pp30) REVERT: E 133 GLU cc_start: 0.8529 (pt0) cc_final: 0.8217 (pt0) REVERT: F 25 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8200 (t0) REVERT: F 50 ILE cc_start: 0.9116 (mm) cc_final: 0.8908 (mt) REVERT: F 84 MET cc_start: 0.8541 (tpp) cc_final: 0.8176 (tpp) REVERT: F 88 TYR cc_start: 0.9100 (m-80) cc_final: 0.8856 (m-80) REVERT: F 91 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8877 (ttmt) REVERT: G 35 ARG cc_start: 0.9207 (mtm110) cc_final: 0.8809 (ttm-80) REVERT: G 81 ARG cc_start: 0.8595 (tpt170) cc_final: 0.8261 (tpt170) REVERT: G 104 GLN cc_start: 0.8757 (mp10) cc_final: 0.8441 (mp10) REVERT: H 77 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8189 (mtm-85) REVERT: H 83 MET cc_start: 0.8898 (tpp) cc_final: 0.8441 (tpp) REVERT: H 85 SER cc_start: 0.8919 (t) cc_final: 0.8614 (t) REVERT: H 89 ASP cc_start: 0.8834 (t0) cc_final: 0.8542 (t0) REVERT: H 141 ARG cc_start: 0.8903 (mtp85) cc_final: 0.8428 (ttm110) outliers start: 31 outliers final: 19 residues processed: 221 average time/residue: 0.3395 time to fit residues: 95.5216 Evaluate side-chains 210 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 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 = 0.3588 r_free = 0.3588 target = 0.082722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.056598 restraints weight = 31088.775| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.89 r_work: 0.2696 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11168 Z= 0.246 Angle : 0.593 10.525 16102 Z= 0.347 Chirality : 0.035 0.266 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.728 177.883 3390 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 4.80 % Allowed : 33.62 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.33), residues: 688 helix: 2.44 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.020 0.001 TYR D 61 ARG 0.006 0.000 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.757 Fit side-chains REVERT: A 50 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7548 (tm-30) REVERT: A 59 GLU cc_start: 0.8251 (pm20) cc_final: 0.7835 (pm20) REVERT: A 94 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8598 (mm-30) REVERT: A 133 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8399 (tt0) REVERT: B 74 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8905 (mm-30) REVERT: B 84 MET cc_start: 0.8428 (tpp) cc_final: 0.8207 (tpp) REVERT: C 24 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8816 (mm110) REVERT: C 25 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.7508 (t80) REVERT: C 56 GLU cc_start: 0.8679 (tt0) cc_final: 0.8260 (tt0) REVERT: C 68 ASN cc_start: 0.8780 (m-40) cc_final: 0.8545 (m-40) REVERT: D 71 GLN cc_start: 0.8993 (pp30) cc_final: 0.8767 (pp30) REVERT: D 137 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8464 (mtmm) REVERT: E 73 GLU cc_start: 0.8906 (tt0) cc_final: 0.8647 (tt0) REVERT: E 133 GLU cc_start: 0.8518 (pt0) cc_final: 0.8195 (pt0) REVERT: F 25 ASN cc_start: 0.9034 (m-40) cc_final: 0.8295 (t0) REVERT: F 84 MET cc_start: 0.8525 (tpp) cc_final: 0.8141 (tpp) REVERT: F 88 TYR cc_start: 0.9120 (m-80) cc_final: 0.8884 (m-80) REVERT: G 35 ARG cc_start: 0.9264 (mtm110) cc_final: 0.8908 (ttm-80) REVERT: G 81 ARG cc_start: 0.8600 (tpt170) cc_final: 0.8285 (tpt170) REVERT: G 104 GLN cc_start: 0.8789 (mp10) cc_final: 0.8474 (mp10) REVERT: H 77 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8184 (mtm-85) REVERT: H 83 MET cc_start: 0.8839 (tpp) cc_final: 0.8484 (tpp) REVERT: H 85 SER cc_start: 0.8920 (t) cc_final: 0.8698 (t) REVERT: H 89 ASP cc_start: 0.8820 (t0) cc_final: 0.8586 (t0) REVERT: H 116 ARG cc_start: 0.8286 (ttt90) cc_final: 0.7899 (ttt90) REVERT: H 141 ARG cc_start: 0.8897 (mtp85) cc_final: 0.8424 (ttm110) outliers start: 28 outliers final: 17 residues processed: 216 average time/residue: 0.3342 time to fit residues: 91.3201 Evaluate side-chains 203 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.084305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057833 restraints weight = 31608.916| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.93 r_work: 0.2736 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11168 Z= 0.201 Angle : 0.589 9.376 16102 Z= 0.343 Chirality : 0.035 0.294 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.654 177.570 3390 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 3.77 % Allowed : 35.51 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.32), residues: 688 helix: 2.53 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.32 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.018 0.001 TYR D 61 ARG 0.006 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7717 (tm-30) REVERT: A 59 GLU cc_start: 0.8278 (pm20) cc_final: 0.7825 (pm20) REVERT: A 94 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8584 (mm-30) REVERT: A 133 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8376 (tt0) REVERT: B 74 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8862 (mm-30) REVERT: B 84 MET cc_start: 0.8412 (tpp) cc_final: 0.8195 (tpp) REVERT: B 98 TYR cc_start: 0.8061 (m-80) cc_final: 0.7694 (m-80) REVERT: C 24 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8749 (mm110) REVERT: C 56 GLU cc_start: 0.8607 (tt0) cc_final: 0.8141 (tt0) REVERT: C 68 ASN cc_start: 0.8748 (m-40) cc_final: 0.8545 (m-40) REVERT: D 71 GLN cc_start: 0.9005 (pp30) cc_final: 0.8701 (pp30) REVERT: D 137 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8380 (mtmm) REVERT: E 73 GLU cc_start: 0.8952 (tt0) cc_final: 0.8713 (tt0) REVERT: E 133 GLU cc_start: 0.8482 (pt0) cc_final: 0.8212 (pt0) REVERT: F 25 ASN cc_start: 0.9029 (m-40) cc_final: 0.8409 (t0) REVERT: F 44 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8460 (mtmm) REVERT: F 84 MET cc_start: 0.8535 (tpp) cc_final: 0.8169 (tpp) REVERT: G 35 ARG cc_start: 0.9247 (mtm110) cc_final: 0.8914 (ttm-80) REVERT: G 71 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.8905 (mmm-85) REVERT: G 81 ARG cc_start: 0.8608 (tpt170) cc_final: 0.8310 (tpt170) REVERT: G 104 GLN cc_start: 0.8789 (mp10) cc_final: 0.8485 (mp10) REVERT: H 77 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8206 (mtm-85) REVERT: H 83 MET cc_start: 0.8811 (tpp) cc_final: 0.8511 (tpp) REVERT: H 85 SER cc_start: 0.8871 (t) cc_final: 0.8569 (t) REVERT: H 89 ASP cc_start: 0.8885 (t0) cc_final: 0.8560 (t0) REVERT: H 141 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8498 (ttm110) outliers start: 22 outliers final: 15 residues processed: 219 average time/residue: 0.3066 time to fit residues: 86.7202 Evaluate side-chains 207 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.3661 r_free = 0.3661 target = 0.085329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057885 restraints weight = 31259.234| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.77 r_work: 0.2822 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11168 Z= 0.198 Angle : 0.606 10.603 16102 Z= 0.348 Chirality : 0.035 0.326 1842 Planarity : 0.005 0.049 1208 Dihedral : 30.634 177.284 3390 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 3.95 % Allowed : 36.36 % Favored : 59.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.32), residues: 688 helix: 2.64 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.17 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.002 0.000 HIS E 113 PHE 0.007 0.001 PHE E 104 TYR 0.019 0.001 TYR D 61 ARG 0.012 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7769 (tm-30) REVERT: A 59 GLU cc_start: 0.8421 (pm20) cc_final: 0.7962 (pm20) REVERT: A 94 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8600 (mm-30) REVERT: A 133 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8362 (tt0) REVERT: B 74 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8920 (mm-30) REVERT: B 84 MET cc_start: 0.8547 (tpp) cc_final: 0.8334 (tpp) REVERT: B 98 TYR cc_start: 0.8237 (m-80) cc_final: 0.7793 (m-80) REVERT: C 24 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8769 (mm110) REVERT: C 56 GLU cc_start: 0.8687 (tt0) cc_final: 0.8211 (tt0) REVERT: D 71 GLN cc_start: 0.9017 (pp30) cc_final: 0.8732 (pp30) REVERT: D 137 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8592 (mtmm) REVERT: E 73 GLU cc_start: 0.8983 (tt0) cc_final: 0.8732 (tt0) REVERT: E 133 GLU cc_start: 0.8623 (pt0) cc_final: 0.8295 (pt0) REVERT: F 25 ASN cc_start: 0.9121 (m-40) cc_final: 0.8433 (t0) REVERT: F 79 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7885 (mttt) REVERT: F 84 MET cc_start: 0.8610 (tpp) cc_final: 0.8298 (tpp) REVERT: G 35 ARG cc_start: 0.9284 (mtm110) cc_final: 0.8984 (ttm-80) REVERT: G 71 ARG cc_start: 0.9239 (mmm-85) cc_final: 0.8951 (mmm-85) REVERT: G 81 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8412 (tpt170) REVERT: G 104 GLN cc_start: 0.8871 (mp10) cc_final: 0.8564 (mp10) REVERT: H 77 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8252 (mtm-85) REVERT: H 85 SER cc_start: 0.8958 (t) cc_final: 0.8646 (t) REVERT: H 89 ASP cc_start: 0.8961 (t0) cc_final: 0.8592 (t0) REVERT: H 141 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8549 (ttm110) outliers start: 23 outliers final: 20 residues processed: 212 average time/residue: 0.3158 time to fit residues: 86.3395 Evaluate side-chains 207 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.081962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054247 restraints weight = 31217.536| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.71 r_work: 0.2731 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11168 Z= 0.361 Angle : 0.666 9.848 16102 Z= 0.381 Chirality : 0.039 0.376 1842 Planarity : 0.005 0.059 1208 Dihedral : 30.985 177.673 3390 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 3.77 % Allowed : 37.05 % Favored : 59.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.32), residues: 688 helix: 2.41 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.30 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 104 TYR 0.017 0.002 TYR F 88 ARG 0.012 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.767 Fit side-chains REVERT: A 50 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7750 (tm-30) REVERT: A 59 GLU cc_start: 0.8496 (pm20) cc_final: 0.8015 (pm20) REVERT: A 94 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8683 (mm-30) REVERT: A 133 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8420 (tt0) REVERT: B 74 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9016 (mm-30) REVERT: B 84 MET cc_start: 0.8527 (tpp) cc_final: 0.8296 (tpp) REVERT: C 19 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8836 (p) REVERT: C 25 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7564 (t80) REVERT: C 56 GLU cc_start: 0.8844 (tt0) cc_final: 0.8468 (tt0) REVERT: D 137 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8616 (mtmm) REVERT: E 133 GLU cc_start: 0.8710 (pt0) cc_final: 0.8431 (pt0) REVERT: F 25 ASN cc_start: 0.9093 (m-40) cc_final: 0.8560 (t0) REVERT: F 84 MET cc_start: 0.8645 (tpp) cc_final: 0.8423 (tpp) REVERT: G 35 ARG cc_start: 0.9301 (mtm110) cc_final: 0.8777 (mtm-85) REVERT: G 81 ARG cc_start: 0.8764 (tpt170) cc_final: 0.8472 (tpt170) REVERT: G 104 GLN cc_start: 0.9064 (mp10) cc_final: 0.8761 (mp10) REVERT: H 77 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8186 (mtm-85) REVERT: H 89 ASP cc_start: 0.8899 (t0) cc_final: 0.8601 (t0) REVERT: H 141 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8542 (ttm110) outliers start: 22 outliers final: 15 residues processed: 211 average time/residue: 0.3169 time to fit residues: 85.4704 Evaluate side-chains 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** F 75 HIS ** 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 = 0.3634 r_free = 0.3634 target = 0.083699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056532 restraints weight = 31374.669| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.73 r_work: 0.2776 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11168 Z= 0.242 Angle : 0.628 9.048 16102 Z= 0.363 Chirality : 0.036 0.344 1842 Planarity : 0.005 0.055 1208 Dihedral : 30.849 177.445 3390 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.60 % Allowed : 37.91 % Favored : 58.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.32), residues: 688 helix: 2.46 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.008 0.001 PHE C 25 TYR 0.018 0.001 TYR B 98 ARG 0.014 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.767 Fit side-chains REVERT: A 50 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7771 (tm-30) REVERT: A 59 GLU cc_start: 0.8457 (pm20) cc_final: 0.8004 (pm20) REVERT: A 94 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8597 (mm-30) REVERT: A 133 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8437 (tt0) REVERT: B 74 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8929 (mm-30) REVERT: B 84 MET cc_start: 0.8565 (tpp) cc_final: 0.8347 (tpp) REVERT: B 98 TYR cc_start: 0.8222 (m-80) cc_final: 0.7721 (m-80) REVERT: C 24 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8773 (mm-40) REVERT: C 25 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 56 GLU cc_start: 0.8776 (tt0) cc_final: 0.8362 (tt0) REVERT: D 137 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8615 (mtmm) REVERT: E 73 GLU cc_start: 0.8938 (tt0) cc_final: 0.8715 (tt0) REVERT: E 133 GLU cc_start: 0.8664 (pt0) cc_final: 0.8365 (pt0) REVERT: F 25 ASN cc_start: 0.9100 (m-40) cc_final: 0.8520 (t0) REVERT: F 79 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7881 (mttt) REVERT: F 84 MET cc_start: 0.8613 (tpp) cc_final: 0.8396 (tpp) REVERT: G 35 ARG cc_start: 0.9315 (mtm110) cc_final: 0.8993 (ttm-80) REVERT: G 71 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8871 (mmm-85) REVERT: G 81 ARG cc_start: 0.8714 (tpt170) cc_final: 0.8429 (tpt170) REVERT: G 104 GLN cc_start: 0.9063 (mp10) cc_final: 0.8820 (mp10) REVERT: H 77 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8210 (mtm-85) REVERT: H 85 SER cc_start: 0.8868 (t) cc_final: 0.8486 (t) REVERT: H 89 ASP cc_start: 0.8910 (t0) cc_final: 0.8550 (t0) REVERT: H 141 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8521 (ttm110) outliers start: 21 outliers final: 18 residues processed: 203 average time/residue: 0.3228 time to fit residues: 85.8096 Evaluate side-chains 205 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.3666 r_free = 0.3666 target = 0.085208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057905 restraints weight = 30888.371| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.75 r_work: 0.2817 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11168 Z= 0.204 Angle : 0.619 8.713 16102 Z= 0.358 Chirality : 0.035 0.345 1842 Planarity : 0.004 0.048 1208 Dihedral : 30.708 176.755 3390 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 2.40 % Allowed : 38.59 % Favored : 59.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.60 (0.32), residues: 688 helix: 2.54 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.19 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.019 0.001 TYR F 88 ARG 0.007 0.000 ARG G 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.815 Fit side-chains REVERT: A 50 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7826 (tm-30) REVERT: A 58 THR cc_start: 0.8622 (p) cc_final: 0.8409 (t) REVERT: A 59 GLU cc_start: 0.8523 (pm20) cc_final: 0.8120 (pm20) REVERT: A 94 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8612 (mm-30) REVERT: A 133 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8416 (tt0) REVERT: B 74 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8844 (mm-30) REVERT: B 84 MET cc_start: 0.8544 (tpp) cc_final: 0.8334 (tpp) REVERT: B 98 TYR cc_start: 0.8129 (m-80) cc_final: 0.7609 (m-80) REVERT: C 24 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8714 (mm110) REVERT: C 56 GLU cc_start: 0.8677 (tt0) cc_final: 0.8211 (tt0) REVERT: C 91 GLU cc_start: 0.9240 (mp0) cc_final: 0.8799 (tp30) REVERT: D 137 LYS cc_start: 0.8831 (mtmm) cc_final: 0.8588 (mtmm) REVERT: E 73 GLU cc_start: 0.8917 (tt0) cc_final: 0.8686 (tt0) REVERT: E 133 GLU cc_start: 0.8597 (pt0) cc_final: 0.8195 (pt0) REVERT: F 25 ASN cc_start: 0.9061 (m-40) cc_final: 0.8454 (t0) REVERT: F 79 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7828 (mttt) REVERT: F 84 MET cc_start: 0.8544 (tpp) cc_final: 0.8313 (tpp) REVERT: G 35 ARG cc_start: 0.9290 (mtm110) cc_final: 0.8981 (ttm-80) REVERT: G 71 ARG cc_start: 0.9194 (mmm-85) cc_final: 0.8947 (mmm-85) REVERT: G 81 ARG cc_start: 0.8708 (tpt170) cc_final: 0.8437 (tpt170) REVERT: G 104 GLN cc_start: 0.9043 (mp10) cc_final: 0.8764 (mp10) REVERT: H 77 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8218 (mtm-85) REVERT: H 85 SER cc_start: 0.8830 (t) cc_final: 0.8534 (t) REVERT: H 89 ASP cc_start: 0.8908 (t0) cc_final: 0.8517 (t0) REVERT: H 141 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8495 (ttm110) outliers start: 14 outliers final: 14 residues processed: 204 average time/residue: 0.3092 time to fit residues: 80.9790 Evaluate side-chains 207 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.3651 r_free = 0.3651 target = 0.084515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056946 restraints weight = 30692.325| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.76 r_work: 0.2808 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11168 Z= 0.230 Angle : 0.628 9.818 16102 Z= 0.361 Chirality : 0.036 0.376 1842 Planarity : 0.004 0.047 1208 Dihedral : 30.734 176.939 3390 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 2.74 % Allowed : 38.25 % Favored : 59.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.62 (0.32), residues: 688 helix: 2.56 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.008 0.001 PHE C 25 TYR 0.024 0.002 TYR F 88 ARG 0.007 0.000 ARG G 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.21 seconds wall clock time: 84 minutes 32.35 seconds (5072.35 seconds total)