Starting phenix.real_space_refine on Sat Aug 23 06:09:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcd_36158/08_2025/8jcd_36158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcd_36158/08_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_36158/08_2025/8jcd_36158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcd_36158/08_2025/8jcd_36158.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcd_36158/08_2025/8jcd_36158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcd_36158/08_2025/8jcd_36158.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.64, per 1000 atoms: 0.25 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: 0.88 Conformation dependent library (CDL) restraints added in 217.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.60 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: 1.95 Time building geometry restraints manager: 1.20 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: 0.510 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.470 ------------------------------------------------------------------------------- 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= 0.153 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.32), 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 ARG 0.009 0.000 ARG F 92 TYR 0.026 0.001 TYR D 61 PHE 0.014 0.001 PHE C 25 TRP 0.008 0.002 TRP D 113 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00334 (11168) covalent geometry : angle 0.57426 (16102) hydrogen bonds : bond 0.09157 ( 694) hydrogen bonds : angle 3.83747 ( 1760) *********************** 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 : 0.304 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: 0.1418 time to fit residues: 41.8958 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 : 0.272 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 D 126 GLN E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.086197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058616 restraints weight = 30784.887| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.95 r_work: 0.2769 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1394 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= 0.148 Angle : 0.564 7.902 16102 Z= 0.332 Chirality : 0.033 0.158 1842 Planarity : 0.004 0.041 1208 Dihedral : 30.345 178.739 3392 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 3.43 % Allowed : 34.48 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.33), residues: 688 helix: 2.24 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.21 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 88 TYR 0.015 0.001 TYR D 61 PHE 0.010 0.001 PHE C 25 TRP 0.007 0.001 TRP D 113 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00316 (11168) covalent geometry : angle 0.56372 (16102) hydrogen bonds : bond 0.03591 ( 694) hydrogen bonds : angle 3.12936 ( 1760) *********************** 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 243 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7527 (tm-30) REVERT: A 59 GLU cc_start: 0.7866 (pm20) cc_final: 0.7466 (pm20) REVERT: A 60 LEU cc_start: 0.9010 (mt) cc_final: 0.8668 (mt) REVERT: A 94 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8678 (mm-30) REVERT: A 133 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8357 (tt0) REVERT: B 74 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8850 (mm-30) REVERT: B 84 MET cc_start: 0.8362 (tpp) cc_final: 0.8093 (tpp) REVERT: B 98 TYR cc_start: 0.8427 (m-10) cc_final: 0.8123 (m-80) REVERT: C 24 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8712 (mm110) REVERT: C 38 ASN cc_start: 0.8903 (t0) cc_final: 0.8651 (t0) REVERT: C 56 GLU cc_start: 0.8511 (tt0) cc_final: 0.8152 (tt0) REVERT: C 68 ASN cc_start: 0.8842 (m-40) cc_final: 0.8387 (m-40) REVERT: C 95 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8539 (tppt) REVERT: E 73 GLU cc_start: 0.9029 (tt0) cc_final: 0.8745 (tt0) REVERT: E 133 GLU cc_start: 0.8440 (pt0) cc_final: 0.8198 (pt0) REVERT: F 25 ASN cc_start: 0.8944 (m-40) cc_final: 0.8124 (t0) REVERT: F 50 ILE cc_start: 0.9199 (mm) cc_final: 0.8967 (mt) REVERT: F 79 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7589 (mttt) REVERT: F 84 MET cc_start: 0.8568 (mpp) cc_final: 0.8147 (tpp) REVERT: F 88 TYR cc_start: 0.9093 (m-10) cc_final: 0.8848 (m-80) REVERT: F 91 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8884 (ttmt) REVERT: G 38 ASN cc_start: 0.9339 (OUTLIER) cc_final: 0.9136 (t0) REVERT: G 81 ARG cc_start: 0.8557 (tpt170) cc_final: 0.8147 (tpt170) REVERT: G 104 GLN cc_start: 0.8655 (mp10) cc_final: 0.8357 (mp10) REVERT: H 77 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8272 (mtm-85) REVERT: H 85 SER cc_start: 0.8798 (t) cc_final: 0.8376 (t) REVERT: H 89 ASP cc_start: 0.8893 (t70) cc_final: 0.8390 (t0) REVERT: H 116 ARG cc_start: 0.8246 (ttt90) cc_final: 0.7808 (ttt90) REVERT: H 141 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8610 (ttm-80) outliers start: 20 outliers final: 9 residues processed: 236 average time/residue: 0.1409 time to fit residues: 42.5804 Evaluate side-chains 211 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 27 VAL 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 38 ASN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 81 SER 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 49 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 93 GLN ** 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 = 0.3638 r_free = 0.3638 target = 0.085422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057848 restraints weight = 31075.378| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.97 r_work: 0.2753 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11168 Z= 0.157 Angle : 0.563 7.703 16102 Z= 0.332 Chirality : 0.034 0.239 1842 Planarity : 0.005 0.061 1208 Dihedral : 30.433 178.405 3390 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.95 % Allowed : 33.28 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.33), residues: 688 helix: 2.37 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 32 TYR 0.016 0.001 TYR D 61 PHE 0.014 0.001 PHE E 78 TRP 0.005 0.001 TRP D 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (11168) covalent geometry : angle 0.56256 (16102) hydrogen bonds : bond 0.03442 ( 694) hydrogen bonds : angle 3.13999 ( 1760) *********************** 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 239 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7574 (tm-30) REVERT: A 59 GLU cc_start: 0.8040 (pm20) cc_final: 0.7598 (pm20) REVERT: A 94 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8625 (mm-30) REVERT: A 133 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8307 (tt0) REVERT: B 23 ARG cc_start: 0.9166 (tpp80) cc_final: 0.8883 (mmp80) REVERT: B 84 MET cc_start: 0.8392 (tpp) cc_final: 0.8134 (tpp) REVERT: B 92 ARG cc_start: 0.9113 (ttp80) cc_final: 0.8661 (mmm-85) REVERT: B 98 TYR cc_start: 0.8638 (m-10) cc_final: 0.8346 (m-80) REVERT: C 24 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8689 (mm110) REVERT: C 38 ASN cc_start: 0.8876 (t0) cc_final: 0.8556 (t0) REVERT: C 56 GLU cc_start: 0.8563 (tt0) cc_final: 0.8183 (tt0) REVERT: C 68 ASN cc_start: 0.8810 (m-40) cc_final: 0.8549 (m-40) REVERT: C 95 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8544 (tppt) REVERT: D 114 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8563 (mm-30) REVERT: D 137 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8393 (mtmm) REVERT: E 133 GLU cc_start: 0.8455 (pt0) cc_final: 0.8228 (pt0) REVERT: F 25 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8176 (t0) REVERT: F 79 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7671 (mttt) REVERT: F 81 VAL cc_start: 0.9434 (t) cc_final: 0.9058 (m) REVERT: F 84 MET cc_start: 0.8563 (tpp) cc_final: 0.8172 (tpp) REVERT: F 88 TYR cc_start: 0.9083 (m-10) cc_final: 0.8869 (m-80) REVERT: F 91 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8782 (ttmt) REVERT: G 71 ARG cc_start: 0.9147 (mmm-85) cc_final: 0.8863 (mmm-85) REVERT: G 81 ARG cc_start: 0.8631 (tpt170) cc_final: 0.8269 (tpt170) REVERT: G 104 GLN cc_start: 0.8703 (mp10) cc_final: 0.8424 (mp10) REVERT: H 77 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8260 (mtm-85) REVERT: H 85 SER cc_start: 0.8760 (t) cc_final: 0.8368 (t) REVERT: H 89 ASP cc_start: 0.8864 (t70) cc_final: 0.8404 (t0) REVERT: H 116 ARG cc_start: 0.8263 (ttt90) cc_final: 0.7754 (ttt90) REVERT: H 132 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7685 (mt-10) REVERT: H 141 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8557 (ttm-80) outliers start: 23 outliers final: 10 residues processed: 227 average time/residue: 0.1424 time to fit residues: 41.2019 Evaluate side-chains 210 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER 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 87 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN 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 33 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 93 GLN ** 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 = 0.3590 r_free = 0.3590 target = 0.082912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.055481 restraints weight = 31643.854| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.96 r_work: 0.2675 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11168 Z= 0.224 Angle : 0.601 9.706 16102 Z= 0.350 Chirality : 0.036 0.282 1842 Planarity : 0.004 0.043 1208 Dihedral : 30.749 178.579 3390 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 4.29 % Allowed : 34.48 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.33), residues: 688 helix: 2.41 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 63 TYR 0.018 0.001 TYR D 61 PHE 0.012 0.001 PHE E 78 TRP 0.002 0.001 TRP H 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00504 (11168) covalent geometry : angle 0.60050 (16102) hydrogen bonds : bond 0.03743 ( 694) hydrogen bonds : angle 3.23696 ( 1760) *********************** 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 228 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7600 (tm-30) REVERT: A 59 GLU cc_start: 0.8188 (pm20) cc_final: 0.7749 (pm20) REVERT: A 94 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8614 (mm-30) REVERT: A 133 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8398 (tt0) REVERT: B 23 ARG cc_start: 0.9215 (tpp80) cc_final: 0.8896 (mmp80) REVERT: B 84 MET cc_start: 0.8400 (tpp) cc_final: 0.8169 (tpp) REVERT: B 98 TYR cc_start: 0.9082 (m-10) cc_final: 0.8843 (m-80) REVERT: C 24 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8815 (mm110) REVERT: C 25 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.7435 (t80) REVERT: C 56 GLU cc_start: 0.8707 (tt0) cc_final: 0.8321 (tt0) REVERT: C 68 ASN cc_start: 0.8767 (m-40) cc_final: 0.8530 (m-40) REVERT: C 95 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8669 (tppt) REVERT: D 71 GLN cc_start: 0.9005 (pp30) cc_final: 0.8790 (pp30) REVERT: E 133 GLU cc_start: 0.8561 (pt0) cc_final: 0.8237 (pt0) REVERT: F 25 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8206 (t0) REVERT: F 50 ILE cc_start: 0.9158 (mm) cc_final: 0.8954 (mt) REVERT: F 79 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7720 (mttt) REVERT: F 84 MET cc_start: 0.8569 (tpp) cc_final: 0.8187 (tpp) REVERT: F 88 TYR cc_start: 0.9110 (m-10) cc_final: 0.8878 (m-80) REVERT: F 91 LYS cc_start: 0.9057 (ttpt) cc_final: 0.8838 (ttmt) REVERT: G 81 ARG cc_start: 0.8700 (tpt170) cc_final: 0.8328 (tpt170) REVERT: G 104 GLN cc_start: 0.8809 (mp10) cc_final: 0.8504 (mp10) REVERT: H 77 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8197 (mtm-85) REVERT: H 85 SER cc_start: 0.8940 (t) cc_final: 0.8641 (t) REVERT: H 89 ASP cc_start: 0.8873 (t70) cc_final: 0.8472 (t0) REVERT: H 141 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8448 (ttm110) outliers start: 25 outliers final: 14 residues processed: 220 average time/residue: 0.1357 time to fit residues: 38.0570 Evaluate side-chains 208 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 47 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 F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN 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 100 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 81 SER 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 78 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 93 GLN ** 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 = 0.3545 r_free = 0.3545 target = 0.080504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053895 restraints weight = 32170.306| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.95 r_work: 0.2626 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11168 Z= 0.274 Angle : 0.644 10.747 16102 Z= 0.372 Chirality : 0.038 0.278 1842 Planarity : 0.005 0.043 1208 Dihedral : 31.043 178.236 3390 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 4.97 % Allowed : 35.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.32), residues: 688 helix: 2.28 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.52 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.023 0.002 TYR D 61 PHE 0.011 0.001 PHE E 78 TRP 0.002 0.001 TRP D 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00622 (11168) covalent geometry : angle 0.64354 (16102) hydrogen bonds : bond 0.04033 ( 694) hydrogen bonds : angle 3.36647 ( 1760) *********************** 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 230 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.235 Fit side-chains REVERT: A 42 ARG cc_start: 0.8432 (ptm160) cc_final: 0.7766 (mpt180) REVERT: A 50 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7624 (tm-30) REVERT: A 59 GLU cc_start: 0.8261 (pm20) cc_final: 0.7865 (pm20) REVERT: A 120 MET cc_start: 0.7651 (mtt) cc_final: 0.7428 (mtt) REVERT: A 133 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8465 (tt0) REVERT: B 23 ARG cc_start: 0.9299 (tpp80) cc_final: 0.8907 (mmp80) REVERT: B 74 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8931 (mm-30) REVERT: B 84 MET cc_start: 0.8415 (tpp) cc_final: 0.8177 (tpp) REVERT: C 19 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8665 (p) REVERT: C 25 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7473 (t80) REVERT: C 56 GLU cc_start: 0.8785 (tt0) cc_final: 0.8440 (tt0) REVERT: C 57 TYR cc_start: 0.8251 (t80) cc_final: 0.7989 (t80) REVERT: C 68 ASN cc_start: 0.8795 (m-40) cc_final: 0.8520 (m-40) REVERT: C 95 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8727 (tppt) REVERT: D 129 LYS cc_start: 0.7805 (pttm) cc_final: 0.7522 (mmmm) REVERT: D 137 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8594 (mtmm) REVERT: D 148 GLN cc_start: 0.8328 (pm20) cc_final: 0.7779 (pp30) REVERT: E 133 GLU cc_start: 0.8575 (pt0) cc_final: 0.8235 (pt0) REVERT: F 25 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8222 (t0) REVERT: F 84 MET cc_start: 0.8544 (tpp) cc_final: 0.8178 (tpp) REVERT: F 88 TYR cc_start: 0.9095 (m-10) cc_final: 0.8886 (m-80) REVERT: F 91 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8867 (ttmt) REVERT: G 35 ARG cc_start: 0.9241 (mtm110) cc_final: 0.8785 (ttm-80) REVERT: G 81 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8310 (tpt170) REVERT: G 104 GLN cc_start: 0.8908 (mp10) cc_final: 0.8585 (mp10) REVERT: H 77 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.8126 (mtm-85) REVERT: H 89 ASP cc_start: 0.8826 (t70) cc_final: 0.8495 (t0) REVERT: H 105 THR cc_start: 0.8983 (t) cc_final: 0.8781 (t) REVERT: H 116 ARG cc_start: 0.8390 (ttt90) cc_final: 0.7990 (ttt90) REVERT: H 132 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7789 (mt-10) REVERT: H 141 ARG cc_start: 0.8909 (mtp85) cc_final: 0.8600 (ttm-80) outliers start: 29 outliers final: 19 residues processed: 219 average time/residue: 0.1322 time to fit residues: 37.3510 Evaluate side-chains 209 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 47 SER 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 25 ASN Chi-restraints excluded: chain F residue 43 VAL 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 G residue 100 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 81 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 34 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 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 = 0.083107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.055735 restraints weight = 31663.598| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.99 r_work: 0.2694 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11168 Z= 0.168 Angle : 0.595 10.698 16102 Z= 0.346 Chirality : 0.035 0.279 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.843 177.605 3390 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 4.80 % Allowed : 34.82 % Favored : 60.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.33), residues: 688 helix: 2.46 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.51 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 32 TYR 0.024 0.002 TYR D 145 PHE 0.007 0.001 PHE E 78 TRP 0.005 0.001 TRP D 113 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00373 (11168) covalent geometry : angle 0.59466 (16102) hydrogen bonds : bond 0.03339 ( 694) hydrogen bonds : angle 3.12640 ( 1760) *********************** 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 226 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7470 (tm-30) REVERT: A 54 TYR cc_start: 0.8053 (m-10) cc_final: 0.7836 (m-80) REVERT: A 59 GLU cc_start: 0.8299 (pm20) cc_final: 0.7837 (pm20) REVERT: A 94 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8765 (mm-30) REVERT: A 133 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8438 (tt0) REVERT: B 74 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8880 (mm-30) REVERT: B 84 MET cc_start: 0.8454 (tpp) cc_final: 0.8236 (tpp) REVERT: C 24 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8727 (mm-40) REVERT: C 25 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7487 (t80) REVERT: C 56 GLU cc_start: 0.8659 (tt0) cc_final: 0.8255 (tt0) REVERT: C 95 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8672 (tppt) REVERT: D 137 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8547 (mtmm) REVERT: D 145 TYR cc_start: 0.8867 (t80) cc_final: 0.8410 (t80) REVERT: E 133 GLU cc_start: 0.8562 (pt0) cc_final: 0.8266 (pt0) REVERT: F 25 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8210 (t0) REVERT: F 84 MET cc_start: 0.8529 (tpp) cc_final: 0.8148 (tpp) REVERT: F 88 TYR cc_start: 0.9118 (m-10) cc_final: 0.8910 (m-80) REVERT: G 35 ARG cc_start: 0.9274 (mtm110) cc_final: 0.8909 (ttm-80) REVERT: G 81 ARG cc_start: 0.8639 (tpt170) cc_final: 0.8300 (tpt170) REVERT: G 92 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8823 (mm-30) REVERT: G 104 GLN cc_start: 0.8921 (mp10) cc_final: 0.8598 (mp10) REVERT: H 77 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8162 (mtm-85) REVERT: H 116 ARG cc_start: 0.8291 (ttt90) cc_final: 0.7872 (ttt90) REVERT: H 141 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8441 (ttm110) outliers start: 28 outliers final: 15 residues processed: 216 average time/residue: 0.1459 time to fit residues: 40.5132 Evaluate side-chains 203 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 101 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN 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 G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 81 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 71 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 0.0570 chunk 68 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 overall best weight: 3.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** 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 = 0.3597 r_free = 0.3597 target = 0.081865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054173 restraints weight = 31253.118| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.74 r_work: 0.2727 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11168 Z= 0.249 Angle : 0.641 8.959 16102 Z= 0.371 Chirality : 0.037 0.320 1842 Planarity : 0.005 0.045 1208 Dihedral : 30.987 177.402 3390 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.92 % Favored : 95.93 % Rotamer: Outliers : 5.49 % Allowed : 33.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.32), residues: 688 helix: 2.37 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.50 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 32 TYR 0.025 0.002 TYR D 61 PHE 0.008 0.001 PHE E 78 TRP 0.002 0.001 TRP H 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00568 (11168) covalent geometry : angle 0.64102 (16102) hydrogen bonds : bond 0.03845 ( 694) hydrogen bonds : angle 3.33172 ( 1760) *********************** 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 221 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.292 Fit side-chains REVERT: A 50 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7743 (tm-30) REVERT: A 59 GLU cc_start: 0.8434 (pm20) cc_final: 0.7978 (pm20) REVERT: A 94 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8787 (mm-30) REVERT: A 120 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7577 (mtt) REVERT: A 133 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8447 (tt0) REVERT: B 84 MET cc_start: 0.8535 (tpp) cc_final: 0.8295 (tpp) REVERT: C 24 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8812 (mm-40) REVERT: C 25 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.7575 (t80) REVERT: C 56 GLU cc_start: 0.8820 (tt0) cc_final: 0.8427 (tt0) REVERT: C 95 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8758 (tppt) REVERT: D 137 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8636 (mtmm) REVERT: E 133 GLU cc_start: 0.8685 (pt0) cc_final: 0.8384 (pt0) REVERT: F 25 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8335 (t0) REVERT: F 84 MET cc_start: 0.8650 (tpp) cc_final: 0.8319 (tpp) REVERT: G 35 ARG cc_start: 0.9309 (mtm110) cc_final: 0.8935 (ttm-80) REVERT: G 81 ARG cc_start: 0.8742 (tpt170) cc_final: 0.8396 (tpt170) REVERT: G 104 GLN cc_start: 0.9068 (mp10) cc_final: 0.8743 (mp10) REVERT: H 77 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8164 (mtm-85) REVERT: H 89 ASP cc_start: 0.8955 (t0) cc_final: 0.8720 (t0) REVERT: H 141 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8513 (ttm110) outliers start: 32 outliers final: 18 residues processed: 211 average time/residue: 0.1293 time to fit residues: 34.9221 Evaluate side-chains 207 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 120 MET 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 E residue 61 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN 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 81 SER 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 72 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 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 = 0.3621 r_free = 0.3621 target = 0.083118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055754 restraints weight = 30943.028| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.69 r_work: 0.2766 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11168 Z= 0.188 Angle : 0.615 8.637 16102 Z= 0.358 Chirality : 0.036 0.313 1842 Planarity : 0.004 0.046 1208 Dihedral : 30.913 177.238 3390 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 3.77 % Allowed : 36.19 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.32), residues: 688 helix: 2.46 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.44 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 116 TYR 0.023 0.002 TYR D 145 PHE 0.007 0.001 PHE C 25 TRP 0.005 0.001 TRP D 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00424 (11168) covalent geometry : angle 0.61467 (16102) hydrogen bonds : bond 0.03445 ( 694) hydrogen bonds : angle 3.19543 ( 1760) *********************** 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 213 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.293 Fit side-chains REVERT: A 50 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7788 (tm-30) REVERT: A 59 GLU cc_start: 0.8455 (pm20) cc_final: 0.7990 (pm20) REVERT: A 94 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8765 (mm-30) REVERT: A 133 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8444 (tt0) REVERT: B 84 MET cc_start: 0.8558 (tpp) cc_final: 0.8338 (tpp) REVERT: C 24 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8766 (mm-40) REVERT: C 25 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.7593 (t80) REVERT: C 56 GLU cc_start: 0.8746 (tt0) cc_final: 0.8340 (tt0) REVERT: C 95 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8714 (tppt) REVERT: C 104 GLN cc_start: 0.8823 (pm20) cc_final: 0.8620 (pm20) REVERT: D 137 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8625 (mtmm) REVERT: E 133 GLU cc_start: 0.8675 (pt0) cc_final: 0.8391 (pt0) REVERT: F 25 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8368 (t0) REVERT: F 84 MET cc_start: 0.8629 (tpp) cc_final: 0.8338 (tpp) REVERT: G 35 ARG cc_start: 0.9306 (mtm110) cc_final: 0.8957 (ttm-80) REVERT: G 71 ARG cc_start: 0.9206 (mmm-85) cc_final: 0.8911 (mmm-85) REVERT: G 81 ARG cc_start: 0.8693 (tpt170) cc_final: 0.8371 (tpt170) REVERT: G 104 GLN cc_start: 0.9035 (mp10) cc_final: 0.8738 (mp10) REVERT: H 77 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8142 (mtm-85) REVERT: H 89 ASP cc_start: 0.8932 (t0) cc_final: 0.8657 (t0) REVERT: H 141 ARG cc_start: 0.8928 (mtp85) cc_final: 0.8481 (ttm110) outliers start: 22 outliers final: 15 residues processed: 204 average time/residue: 0.1442 time to fit residues: 37.7911 Evaluate side-chains 203 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 71 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 81 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 37 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 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 = 0.3663 r_free = 0.3663 target = 0.085190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.057961 restraints weight = 30894.831| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.73 r_work: 0.2824 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11168 Z= 0.155 Angle : 0.613 9.961 16102 Z= 0.354 Chirality : 0.035 0.327 1842 Planarity : 0.005 0.047 1208 Dihedral : 30.716 176.628 3390 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 2.06 % Allowed : 37.74 % Favored : 60.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.32), residues: 688 helix: 2.57 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.39 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 116 TYR 0.019 0.001 TYR D 61 PHE 0.007 0.001 PHE C 25 TRP 0.008 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00340 (11168) covalent geometry : angle 0.61296 (16102) hydrogen bonds : bond 0.03244 ( 694) hydrogen bonds : angle 3.07182 ( 1760) *********************** 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 217 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7801 (tm-30) REVERT: A 52 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8719 (ttp-170) REVERT: A 58 THR cc_start: 0.8669 (p) cc_final: 0.8442 (t) REVERT: A 59 GLU cc_start: 0.8474 (pm20) cc_final: 0.8050 (pm20) REVERT: A 94 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8738 (mm-30) REVERT: A 133 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8443 (tt0) REVERT: B 84 MET cc_start: 0.8528 (tpp) cc_final: 0.8316 (tpp) REVERT: C 24 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8678 (mm-40) REVERT: C 56 GLU cc_start: 0.8671 (tt0) cc_final: 0.8227 (tt0) REVERT: C 95 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8661 (tppt) REVERT: C 104 GLN cc_start: 0.8864 (pm20) cc_final: 0.8614 (pm20) REVERT: D 137 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8583 (mtmm) REVERT: E 133 GLU cc_start: 0.8604 (pt0) cc_final: 0.8303 (pt0) REVERT: F 25 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8398 (t0) REVERT: F 79 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7879 (mttt) REVERT: F 84 MET cc_start: 0.8642 (tpp) cc_final: 0.8405 (tpp) REVERT: G 71 ARG cc_start: 0.9212 (mmm-85) cc_final: 0.8957 (mmm-85) REVERT: G 81 ARG cc_start: 0.8686 (tpt170) cc_final: 0.8391 (tpt170) REVERT: G 104 GLN cc_start: 0.8974 (mp10) cc_final: 0.8719 (mp10) REVERT: H 77 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8178 (mtm-85) REVERT: H 89 ASP cc_start: 0.8925 (t0) cc_final: 0.8642 (t0) REVERT: H 141 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8490 (ttm110) outliers start: 12 outliers final: 9 residues processed: 210 average time/residue: 0.1406 time to fit residues: 37.7014 Evaluate side-chains 205 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 47 SER 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 F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN 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 32 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 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 = 0.3652 r_free = 0.3652 target = 0.084616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057316 restraints weight = 30788.357| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.74 r_work: 0.2801 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11168 Z= 0.175 Angle : 0.627 9.659 16102 Z= 0.360 Chirality : 0.036 0.373 1842 Planarity : 0.005 0.062 1208 Dihedral : 30.775 176.926 3390 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 2.06 % Allowed : 38.42 % Favored : 59.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.32), residues: 688 helix: 2.50 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.36 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 116 TYR 0.009 0.001 TYR F 98 PHE 0.008 0.001 PHE E 104 TRP 0.005 0.001 TRP D 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (11168) covalent geometry : angle 0.62731 (16102) hydrogen bonds : bond 0.03377 ( 694) hydrogen bonds : angle 3.14290 ( 1760) ********************** 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 208 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.256 Fit side-chains REVERT: A 50 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7796 (tm-30) REVERT: A 59 GLU cc_start: 0.8512 (pm20) cc_final: 0.8067 (pm20) REVERT: A 94 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8759 (mm-30) REVERT: A 133 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8442 (tt0) REVERT: B 84 MET cc_start: 0.8565 (tpp) cc_final: 0.8352 (tpp) REVERT: C 24 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8703 (mm-40) REVERT: C 56 GLU cc_start: 0.8719 (tt0) cc_final: 0.8294 (tt0) REVERT: C 95 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8715 (tppt) REVERT: C 104 GLN cc_start: 0.8847 (pm20) cc_final: 0.8620 (pm20) REVERT: D 137 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8598 (mtmm) REVERT: E 133 GLU cc_start: 0.8612 (pt0) cc_final: 0.8320 (pt0) REVERT: F 25 ASN cc_start: 0.9056 (m-40) cc_final: 0.8409 (t0) REVERT: F 79 LYS cc_start: 0.8268 (mtmt) cc_final: 0.8043 (mttt) REVERT: F 84 MET cc_start: 0.8668 (tpp) cc_final: 0.8460 (tpp) REVERT: G 35 ARG cc_start: 0.9296 (mtm110) cc_final: 0.8987 (ttm-80) REVERT: G 71 ARG cc_start: 0.9231 (mmm-85) cc_final: 0.8978 (mmm-85) REVERT: G 81 ARG cc_start: 0.8742 (tpt170) cc_final: 0.8414 (tpt170) REVERT: G 104 GLN cc_start: 0.9031 (mp10) cc_final: 0.8714 (mp10) REVERT: H 77 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8130 (mtm-85) REVERT: H 89 ASP cc_start: 0.8947 (t0) cc_final: 0.8686 (t0) REVERT: H 141 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8462 (ttm110) outliers start: 12 outliers final: 9 residues processed: 202 average time/residue: 0.1373 time to fit residues: 35.7636 Evaluate side-chains 200 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 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 13 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 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 = 0.3658 r_free = 0.3658 target = 0.084814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057505 restraints weight = 31037.631| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.75 r_work: 0.2813 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11168 Z= 0.168 Angle : 0.622 10.062 16102 Z= 0.357 Chirality : 0.036 0.374 1842 Planarity : 0.005 0.057 1208 Dihedral : 30.723 176.997 3390 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 2.40 % Allowed : 37.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.32), residues: 688 helix: 2.55 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 116 TYR 0.015 0.001 TYR F 88 PHE 0.008 0.001 PHE C 25 TRP 0.013 0.002 TRP H 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00376 (11168) covalent geometry : angle 0.62227 (16102) hydrogen bonds : bond 0.03290 ( 694) hydrogen bonds : angle 3.13227 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.38 seconds wall clock time: 42 minutes 25.54 seconds (2545.54 seconds total)