Starting phenix.real_space_refine on Thu May 1 03:39:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcd_36158/05_2025/8jcd_36158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcd_36158/05_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_36158/05_2025/8jcd_36158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcd_36158/05_2025/8jcd_36158.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcd_36158/05_2025/8jcd_36158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcd_36158/05_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-5669/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: 5.91, per 1000 atoms: 0.56 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: 2.85 Conformation dependent library (CDL) restraints added in 725.9 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: 4.98 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: 3.66 Time building geometry restraints manager: 3.37 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.260 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.09157 ( 694) hydrogen bonds : angle 3.83747 ( 1760) covalent geometry : bond 0.00334 (11168) covalent geometry : angle 0.57426 (16102) *********************** 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 : 0.812 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: 0.3300 time to fit residues: 97.4942 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 : 0.885 ------------------------------------------------------------------------------- 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: 3.9990 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: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3579 r_free = 0.3579 target = 0.082487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054844 restraints weight = 30878.605| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.91 r_work: 0.2667 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11168 Z= 0.243 Angle : 0.610 7.669 16102 Z= 0.357 Chirality : 0.036 0.170 1842 Planarity : 0.004 0.040 1208 Dihedral : 30.627 178.949 3392 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 5.15 % Allowed : 35.16 % 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: 2.19 (0.33), residues: 688 helix: 2.18 (0.23), residues: 537 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.003 0.001 HIS E 113 PHE 0.010 0.001 PHE C 25 TYR 0.020 0.002 TYR D 61 ARG 0.007 0.001 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 694) hydrogen bonds : angle 3.32792 ( 1760) covalent geometry : bond 0.00547 (11168) covalent geometry : angle 0.60977 (16102) *********************** 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 237 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7525 (tm-30) REVERT: A 58 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8229 (t) REVERT: A 59 GLU cc_start: 0.7990 (pm20) cc_final: 0.7633 (pm20) REVERT: A 133 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8448 (tt0) REVERT: B 84 MET cc_start: 0.8343 (tpp) cc_final: 0.7996 (tpp) REVERT: C 24 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8767 (mm110) REVERT: C 38 ASN cc_start: 0.8865 (t0) cc_final: 0.8491 (t0) REVERT: C 56 GLU cc_start: 0.8621 (tt0) cc_final: 0.8285 (tt0) REVERT: C 68 ASN cc_start: 0.8903 (m-40) cc_final: 0.8443 (m-40) REVERT: C 95 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8633 (tppt) REVERT: D 129 LYS cc_start: 0.7729 (pttm) cc_final: 0.7510 (mmmm) REVERT: E 94 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8622 (mm-30) REVERT: E 133 GLU cc_start: 0.8489 (pt0) cc_final: 0.8244 (pt0) REVERT: F 25 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8180 (t0) REVERT: F 50 ILE cc_start: 0.9184 (mm) cc_final: 0.8977 (mt) REVERT: F 53 GLU cc_start: 0.8954 (tp30) cc_final: 0.8707 (tp30) REVERT: F 84 MET cc_start: 0.8536 (tpp) cc_final: 0.8154 (tpp) REVERT: F 88 TYR cc_start: 0.9070 (m-80) cc_final: 0.8809 (m-80) REVERT: F 91 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8966 (ttmt) REVERT: F 98 TYR cc_start: 0.9176 (m-10) cc_final: 0.8933 (m-80) REVERT: G 41 GLU cc_start: 0.9270 (mt-10) cc_final: 0.9044 (mt-10) REVERT: G 81 ARG cc_start: 0.8591 (tpt170) cc_final: 0.8212 (tpt170) REVERT: G 104 GLN cc_start: 0.8714 (mp10) cc_final: 0.8451 (mp10) REVERT: H 85 SER cc_start: 0.8949 (t) cc_final: 0.8646 (t) REVERT: H 89 ASP cc_start: 0.8922 (t70) cc_final: 0.8639 (t0) REVERT: H 141 ARG cc_start: 0.8900 (mtp85) cc_final: 0.8417 (ttm110) outliers start: 30 outliers final: 13 residues processed: 228 average time/residue: 0.3296 time to fit residues: 95.6583 Evaluate side-chains 201 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 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 27 VAL 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: 0.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 0.0970 chunk 79 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** 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 = 0.3627 r_free = 0.3627 target = 0.084696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057205 restraints weight = 31006.116| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.96 r_work: 0.2742 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1710 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 : 0.574 8.709 16102 Z= 0.336 Chirality : 0.034 0.193 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.531 178.141 3390 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.60 % Allowed : 34.99 % Favored : 61.41 % 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: 2.46 (0.33), residues: 688 helix: 2.39 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.017 0.001 TYR D 61 ARG 0.006 0.001 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 694) hydrogen bonds : angle 3.11052 ( 1760) covalent geometry : bond 0.00319 (11168) covalent geometry : angle 0.57375 (16102) *********************** 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 234 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7590 (tm-30) REVERT: A 59 GLU cc_start: 0.8140 (pm20) cc_final: 0.7701 (pm20) REVERT: A 94 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8859 (mm-30) REVERT: A 133 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8371 (tt0) REVERT: B 74 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8857 (mm-30) REVERT: B 84 MET cc_start: 0.8381 (tpp) cc_final: 0.8115 (tpp) REVERT: B 92 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8642 (mmm-85) REVERT: C 24 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8728 (mm110) REVERT: C 38 ASN cc_start: 0.8857 (t0) cc_final: 0.8640 (t0) REVERT: C 56 GLU cc_start: 0.8581 (tt0) cc_final: 0.8156 (tt0) REVERT: C 68 ASN cc_start: 0.8836 (m-40) cc_final: 0.8561 (m-40) REVERT: C 95 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8515 (tppt) REVERT: D 137 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8401 (mtmm) REVERT: E 73 GLU cc_start: 0.8980 (tt0) cc_final: 0.8660 (tt0) REVERT: E 133 GLU cc_start: 0.8498 (pt0) cc_final: 0.8249 (pt0) REVERT: F 25 ASN cc_start: 0.8992 (m-40) cc_final: 0.8179 (t0) REVERT: F 84 MET cc_start: 0.8579 (tpp) cc_final: 0.8181 (tpp) REVERT: F 88 TYR cc_start: 0.9092 (m-10) cc_final: 0.8858 (m-80) REVERT: F 91 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8841 (ttmt) REVERT: G 41 GLU cc_start: 0.9243 (mt-10) cc_final: 0.9024 (mt-10) REVERT: G 81 ARG cc_start: 0.8592 (tpt170) cc_final: 0.8263 (tpt170) REVERT: G 104 GLN cc_start: 0.8780 (mp10) cc_final: 0.8477 (mp10) REVERT: H 77 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8073 (mtm-85) REVERT: H 85 SER cc_start: 0.8831 (t) cc_final: 0.8625 (t) REVERT: H 89 ASP cc_start: 0.8862 (t70) cc_final: 0.8488 (t0) REVERT: H 141 ARG cc_start: 0.8983 (mtp85) cc_final: 0.8665 (ttm-80) outliers start: 21 outliers final: 11 residues processed: 225 average time/residue: 0.3082 time to fit residues: 89.0097 Evaluate side-chains 208 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 63 LEU 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 G residue 83 LEU Chi-restraints excluded: chain G residue 100 VAL 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: 2.9990 chunk 90 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.1500 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057938 restraints weight = 30908.148| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.96 r_work: 0.2751 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1991 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= 0.154 Angle : 0.565 9.275 16102 Z= 0.332 Chirality : 0.034 0.264 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.562 177.698 3390 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.07 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: 2.52 (0.32), residues: 688 helix: 2.45 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 113 HIS 0.002 0.001 HIS E 113 PHE 0.006 0.001 PHE E 104 TYR 0.015 0.001 TYR D 61 ARG 0.006 0.001 ARG H 116 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 694) hydrogen bonds : angle 3.05237 ( 1760) covalent geometry : bond 0.00338 (11168) covalent geometry : angle 0.56492 (16102) *********************** 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: 22 poor density : 206 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7611 (tm-30) REVERT: A 59 GLU cc_start: 0.8226 (pm20) cc_final: 0.7798 (pm20) REVERT: A 94 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8763 (mm-30) REVERT: A 133 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8343 (tt0) REVERT: B 74 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8818 (mm-30) REVERT: B 84 MET cc_start: 0.8388 (tpp) cc_final: 0.8141 (tpp) REVERT: B 98 TYR cc_start: 0.8163 (m-80) cc_final: 0.7943 (m-80) REVERT: C 24 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8745 (mm110) REVERT: C 56 GLU cc_start: 0.8652 (tt0) cc_final: 0.8229 (tt0) REVERT: C 95 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8551 (tppt) REVERT: D 71 GLN cc_start: 0.9000 (pp30) cc_final: 0.8779 (pp30) REVERT: D 137 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8380 (mtmm) REVERT: E 73 GLU cc_start: 0.8887 (tt0) cc_final: 0.8644 (tt0) REVERT: E 133 GLU cc_start: 0.8574 (pt0) cc_final: 0.8232 (pt0) REVERT: F 25 ASN cc_start: 0.8978 (m-40) cc_final: 0.8209 (t0) REVERT: F 50 ILE cc_start: 0.9138 (mm) cc_final: 0.8915 (mt) REVERT: F 84 MET cc_start: 0.8558 (tpp) cc_final: 0.8159 (tpp) REVERT: G 71 ARG cc_start: 0.9166 (mmm-85) cc_final: 0.8880 (mmm-85) REVERT: G 81 ARG cc_start: 0.8667 (tpt170) cc_final: 0.8343 (tpt170) REVERT: G 104 GLN cc_start: 0.8765 (mp10) cc_final: 0.8464 (mp10) REVERT: H 77 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8053 (mtm-85) REVERT: H 83 MET cc_start: 0.8808 (tpp) cc_final: 0.8405 (tpp) REVERT: H 85 SER cc_start: 0.8854 (t) cc_final: 0.8594 (t) REVERT: H 89 ASP cc_start: 0.8883 (t70) cc_final: 0.8446 (t0) REVERT: H 141 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8580 (ttm110) outliers start: 22 outliers final: 13 residues processed: 220 average time/residue: 0.3215 time to fit residues: 90.4084 Evaluate side-chains 210 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 E residue 61 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 100 VAL 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 8 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.083443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055769 restraints weight = 30912.836| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.96 r_work: 0.2711 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2116 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= 0.189 Angle : 0.586 10.162 16102 Z= 0.343 Chirality : 0.035 0.312 1842 Planarity : 0.004 0.046 1208 Dihedral : 30.687 178.078 3390 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.77 % Allowed : 35.33 % 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: 2.57 (0.33), residues: 688 helix: 2.49 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE H 58 TYR 0.020 0.002 TYR D 61 ARG 0.006 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 694) hydrogen bonds : angle 3.13596 ( 1760) covalent geometry : bond 0.00424 (11168) covalent geometry : angle 0.58593 (16102) *********************** 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: 22 poor density : 203 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7611 (tm-30) REVERT: A 52 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8649 (ttp-170) REVERT: A 59 GLU cc_start: 0.8236 (pm20) cc_final: 0.7814 (pm20) REVERT: A 94 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8571 (mm-30) REVERT: A 133 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8359 (tt0) REVERT: B 74 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8795 (mm-30) REVERT: B 84 MET cc_start: 0.8388 (tpp) cc_final: 0.8134 (tpp) REVERT: C 24 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8783 (mm110) REVERT: C 25 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7506 (t80) REVERT: C 56 GLU cc_start: 0.8685 (tt0) cc_final: 0.8303 (tt0) REVERT: C 95 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8572 (tppt) REVERT: D 137 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8395 (mtmm) REVERT: E 73 GLU cc_start: 0.8926 (tt0) cc_final: 0.8718 (tt0) REVERT: E 133 GLU cc_start: 0.8556 (pt0) cc_final: 0.8239 (pt0) REVERT: F 25 ASN cc_start: 0.9019 (m-40) cc_final: 0.8190 (t0) REVERT: F 50 ILE cc_start: 0.9132 (mm) cc_final: 0.8932 (mt) REVERT: F 84 MET cc_start: 0.8513 (tpp) cc_final: 0.8227 (tpp) REVERT: G 35 ARG cc_start: 0.9252 (mtm110) cc_final: 0.8918 (ttm-80) REVERT: G 38 ASN cc_start: 0.9269 (t0) cc_final: 0.9067 (t0) REVERT: G 41 GLU cc_start: 0.9259 (mt-10) cc_final: 0.9004 (mt-10) REVERT: G 81 ARG cc_start: 0.8663 (tpt170) cc_final: 0.8323 (tpt170) REVERT: G 104 GLN cc_start: 0.8811 (mp10) cc_final: 0.8506 (mp10) REVERT: H 83 MET cc_start: 0.8829 (tpp) cc_final: 0.8465 (tpp) REVERT: H 85 SER cc_start: 0.8928 (t) cc_final: 0.8668 (t) REVERT: H 89 ASP cc_start: 0.8866 (t70) cc_final: 0.8633 (t0) REVERT: H 141 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8405 (ttm110) outliers start: 22 outliers final: 16 residues processed: 219 average time/residue: 0.3096 time to fit residues: 86.8400 Evaluate side-chains 213 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU 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 100 VAL 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 5 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 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 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 = 0.3617 r_free = 0.3617 target = 0.084093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.056445 restraints weight = 31293.461| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.99 r_work: 0.2731 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2266 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= 0.169 Angle : 0.585 9.309 16102 Z= 0.342 Chirality : 0.035 0.306 1842 Planarity : 0.004 0.047 1208 Dihedral : 30.632 177.896 3390 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 3.60 % Allowed : 36.19 % 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 (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: 2.52 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.22 (0.47), 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 0.019 0.001 TYR D 61 ARG 0.007 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 694) hydrogen bonds : angle 3.06377 ( 1760) covalent geometry : bond 0.00376 (11168) covalent geometry : angle 0.58477 (16102) *********************** 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 225 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.728 Fit side-chains REVERT: A 50 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7612 (tm-30) REVERT: A 59 GLU cc_start: 0.8270 (pm20) cc_final: 0.7851 (pm20) REVERT: A 94 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 133 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8373 (tt0) REVERT: B 74 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8809 (mm-30) REVERT: B 84 MET cc_start: 0.8405 (tpp) cc_final: 0.8159 (tpp) REVERT: C 24 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8775 (mm110) REVERT: C 25 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.7501 (t80) REVERT: C 56 GLU cc_start: 0.8679 (tt0) cc_final: 0.8301 (tt0) REVERT: C 95 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8523 (tppt) REVERT: D 137 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8393 (mtmm) REVERT: E 133 GLU cc_start: 0.8559 (pt0) cc_final: 0.8227 (pt0) REVERT: F 25 ASN cc_start: 0.9034 (m-40) cc_final: 0.8241 (t0) REVERT: F 84 MET cc_start: 0.8516 (tpp) cc_final: 0.8274 (tpp) REVERT: G 35 ARG cc_start: 0.9253 (mtm110) cc_final: 0.8934 (ttm-80) REVERT: G 71 ARG cc_start: 0.9167 (mmm-85) cc_final: 0.8867 (mmm-85) REVERT: G 81 ARG cc_start: 0.8676 (tpt170) cc_final: 0.8355 (tpt170) REVERT: G 104 GLN cc_start: 0.8828 (mp10) cc_final: 0.8524 (mp10) REVERT: H 77 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8002 (mtm-85) REVERT: H 83 MET cc_start: 0.8838 (tpp) cc_final: 0.8542 (tpp) REVERT: H 85 SER cc_start: 0.8907 (t) cc_final: 0.8602 (t) REVERT: H 89 ASP cc_start: 0.8835 (t70) cc_final: 0.8389 (t0) REVERT: H 141 ARG cc_start: 0.8882 (mtp85) cc_final: 0.8441 (ttm110) outliers start: 21 outliers final: 15 residues processed: 217 average time/residue: 0.3210 time to fit residues: 88.4279 Evaluate side-chains 210 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 E residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU 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 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 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.0270 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 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: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.086753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059569 restraints weight = 31344.038| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.76 r_work: 0.2853 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11168 Z= 0.145 Angle : 0.595 9.332 16102 Z= 0.343 Chirality : 0.034 0.325 1842 Planarity : 0.004 0.047 1208 Dihedral : 30.530 177.356 3390 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 3.26 % Allowed : 36.54 % 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 (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: 2.75 (0.32), residues: 688 helix: 2.64 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.10 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.017 0.001 TYR F 88 ARG 0.008 0.001 ARG H 116 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 694) hydrogen bonds : angle 2.98128 ( 1760) covalent geometry : bond 0.00313 (11168) covalent geometry : angle 0.59469 (16102) *********************** 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 226 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7682 (tm-30) REVERT: A 52 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.8553 (mtm-85) REVERT: A 59 GLU cc_start: 0.8413 (pm20) cc_final: 0.7982 (pm20) REVERT: A 94 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8574 (mm-30) REVERT: A 133 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8337 (tt0) REVERT: B 74 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8860 (mm-30) REVERT: B 84 MET cc_start: 0.8499 (tpp) cc_final: 0.8272 (tpp) REVERT: B 98 TYR cc_start: 0.8066 (m-80) cc_final: 0.7477 (m-80) REVERT: C 24 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8710 (mm110) REVERT: C 56 GLU cc_start: 0.8672 (tt0) cc_final: 0.8248 (tt0) REVERT: C 95 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8524 (tppt) REVERT: D 137 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8489 (mtmm) REVERT: E 73 GLU cc_start: 0.8972 (tt0) cc_final: 0.8651 (tt0) REVERT: E 108 ASN cc_start: 0.8543 (t160) cc_final: 0.8247 (t0) REVERT: E 131 ARG cc_start: 0.9129 (mmm-85) cc_final: 0.8872 (mmm-85) REVERT: E 133 GLU cc_start: 0.8560 (pt0) cc_final: 0.8240 (pt0) REVERT: F 84 MET cc_start: 0.8577 (tpp) cc_final: 0.8362 (tpp) REVERT: G 71 ARG cc_start: 0.9239 (mmm-85) cc_final: 0.8965 (mmm-85) REVERT: G 81 ARG cc_start: 0.8719 (tpt170) cc_final: 0.8403 (tpt170) REVERT: G 104 GLN cc_start: 0.8833 (mp10) cc_final: 0.8532 (mp10) REVERT: H 77 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8060 (mtm-85) REVERT: H 85 SER cc_start: 0.8876 (t) cc_final: 0.8542 (t) REVERT: H 89 ASP cc_start: 0.8865 (t70) cc_final: 0.8394 (t0) REVERT: H 141 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8651 (ttm-80) outliers start: 19 outliers final: 14 residues processed: 220 average time/residue: 0.3052 time to fit residues: 86.2002 Evaluate side-chains 212 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 E residue 61 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU 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 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: 1.9990 chunk 90 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 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 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 = 0.3614 r_free = 0.3614 target = 0.082482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.054832 restraints weight = 31166.844| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.71 r_work: 0.2740 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11168 Z= 0.266 Angle : 0.662 9.326 16102 Z= 0.379 Chirality : 0.039 0.383 1842 Planarity : 0.005 0.046 1208 Dihedral : 30.906 177.690 3390 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 3.26 % Allowed : 37.91 % Favored : 58.83 % 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: 2.51 (0.32), residues: 688 helix: 2.47 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 113 HIS 0.002 0.001 HIS E 113 PHE 0.008 0.001 PHE E 104 TYR 0.019 0.002 TYR B 98 ARG 0.008 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 694) hydrogen bonds : angle 3.28618 ( 1760) covalent geometry : bond 0.00607 (11168) covalent geometry : angle 0.66180 (16102) *********************** 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 220 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.744 Fit side-chains REVERT: A 50 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7766 (tm-30) REVERT: A 52 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8542 (mtm-85) REVERT: A 59 GLU cc_start: 0.8507 (pm20) cc_final: 0.8069 (pm20) REVERT: A 94 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8854 (tp30) REVERT: A 133 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8426 (tt0) REVERT: B 74 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8948 (mm-30) REVERT: B 84 MET cc_start: 0.8521 (tpp) cc_final: 0.8261 (tpp) REVERT: C 24 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8843 (mm-40) REVERT: C 25 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.7597 (t80) REVERT: C 56 GLU cc_start: 0.8841 (tt0) cc_final: 0.8478 (tt0) REVERT: C 95 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8601 (tppt) REVERT: D 137 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8551 (mtmm) REVERT: E 133 GLU cc_start: 0.8676 (pt0) cc_final: 0.8356 (pt0) REVERT: F 84 MET cc_start: 0.8627 (tpp) cc_final: 0.8396 (tpp) REVERT: G 35 ARG cc_start: 0.9304 (mtm110) cc_final: 0.8955 (ttm-80) REVERT: G 81 ARG cc_start: 0.8744 (tpt170) cc_final: 0.8415 (tpt170) REVERT: G 104 GLN cc_start: 0.9047 (mp10) cc_final: 0.8725 (mp10) REVERT: H 77 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8252 (mtm-85) REVERT: H 84 ASP cc_start: 0.8683 (t0) cc_final: 0.8453 (t0) REVERT: H 85 SER cc_start: 0.9098 (t) cc_final: 0.8669 (t) REVERT: H 89 ASP cc_start: 0.8912 (t70) cc_final: 0.8667 (t0) REVERT: H 141 ARG cc_start: 0.8960 (mtp85) cc_final: 0.8507 (ttm110) outliers start: 19 outliers final: 13 residues processed: 213 average time/residue: 0.3285 time to fit residues: 88.8301 Evaluate side-chains 205 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 E residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE 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 55 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.084616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057091 restraints weight = 31126.016| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.77 r_work: 0.2804 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11168 Z= 0.170 Angle : 0.623 8.342 16102 Z= 0.361 Chirality : 0.036 0.352 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.732 177.425 3390 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 2.40 % Allowed : 38.94 % Favored : 58.66 % 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: 2.56 (0.32), residues: 688 helix: 2.53 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 161 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 0.020 0.002 TYR F 88 ARG 0.008 0.001 ARG H 116 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 694) hydrogen bonds : angle 3.08981 ( 1760) covalent geometry : bond 0.00383 (11168) covalent geometry : angle 0.62338 (16102) *********************** 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: 14 poor density : 196 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7846 (tm-30) REVERT: A 59 GLU cc_start: 0.8534 (pm20) cc_final: 0.8054 (pm20) REVERT: A 133 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8428 (tt0) REVERT: B 74 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8896 (mm-30) REVERT: B 84 MET cc_start: 0.8541 (tpp) cc_final: 0.8306 (tpp) REVERT: B 98 TYR cc_start: 0.8300 (m-80) cc_final: 0.8049 (m-80) REVERT: C 24 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8777 (mm-40) REVERT: C 25 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7605 (t80) REVERT: C 56 GLU cc_start: 0.8737 (tt0) cc_final: 0.8327 (tt0) REVERT: C 95 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8596 (tppt) REVERT: D 137 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8544 (mtmm) REVERT: E 73 GLU cc_start: 0.8944 (tt0) cc_final: 0.8710 (tt0) REVERT: E 97 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: E 133 GLU cc_start: 0.8567 (pt0) cc_final: 0.8223 (pt0) REVERT: F 84 MET cc_start: 0.8561 (tpp) cc_final: 0.8299 (tpp) REVERT: G 50 TYR cc_start: 0.8721 (t80) cc_final: 0.8379 (t80) REVERT: G 71 ARG cc_start: 0.9137 (mmm-85) cc_final: 0.8849 (mmm-85) REVERT: G 81 ARG cc_start: 0.8728 (tpt170) cc_final: 0.8418 (tpt170) REVERT: G 104 GLN cc_start: 0.9037 (mp10) cc_final: 0.8737 (mp10) REVERT: H 77 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8028 (mtm-85) REVERT: H 85 SER cc_start: 0.8993 (t) cc_final: 0.8607 (t) REVERT: H 89 ASP cc_start: 0.8880 (t70) cc_final: 0.8658 (t0) REVERT: H 141 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8471 (ttm110) outliers start: 14 outliers final: 9 residues processed: 204 average time/residue: 0.3072 time to fit residues: 80.6748 Evaluate side-chains 203 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 E residue 97 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE 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: 0.6980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3680 r_free = 0.3680 target = 0.086184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059264 restraints weight = 30872.508| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.75 r_work: 0.2851 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11168 Z= 0.157 Angle : 0.624 9.163 16102 Z= 0.358 Chirality : 0.035 0.357 1842 Planarity : 0.005 0.056 1208 Dihedral : 30.607 176.773 3390 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 1.89 % Allowed : 38.94 % 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: 2.55 (0.32), residues: 688 helix: 2.53 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 113 HIS 0.002 0.000 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.017 0.001 TYR D 145 ARG 0.012 0.001 ARG H 116 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 694) hydrogen bonds : angle 3.03812 ( 1760) covalent geometry : bond 0.00349 (11168) covalent geometry : angle 0.62410 (16102) ********************** 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 211 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7876 (tm-30) REVERT: A 59 GLU cc_start: 0.8559 (pm20) cc_final: 0.8129 (pm20) REVERT: A 133 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8373 (tt0) REVERT: B 74 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8881 (mm-30) REVERT: B 84 MET cc_start: 0.8559 (tpp) cc_final: 0.8330 (tpp) REVERT: B 98 TYR cc_start: 0.8245 (m-80) cc_final: 0.7827 (m-80) REVERT: C 24 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8714 (mm110) REVERT: C 56 GLU cc_start: 0.8698 (tt0) cc_final: 0.8279 (tt0) REVERT: C 95 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8576 (tppt) REVERT: D 137 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8617 (mtmm) REVERT: E 73 GLU cc_start: 0.8913 (tt0) cc_final: 0.8656 (tt0) REVERT: E 133 GLU cc_start: 0.8508 (pt0) cc_final: 0.7990 (pt0) REVERT: G 50 TYR cc_start: 0.8578 (t80) cc_final: 0.8208 (t80) REVERT: G 71 ARG cc_start: 0.9184 (mmm-85) cc_final: 0.8946 (mmm-85) REVERT: G 81 ARG cc_start: 0.8758 (tpt170) cc_final: 0.8454 (tpt170) REVERT: G 104 GLN cc_start: 0.9067 (mp10) cc_final: 0.8758 (mp10) REVERT: H 77 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8050 (mtm-85) REVERT: H 85 SER cc_start: 0.8863 (t) cc_final: 0.8426 (t) REVERT: H 89 ASP cc_start: 0.8874 (t70) cc_final: 0.8420 (t0) REVERT: H 105 THR cc_start: 0.8875 (t) cc_final: 0.8645 (t) REVERT: H 116 ARG cc_start: 0.8277 (ttt90) cc_final: 0.8021 (mtp85) REVERT: H 141 ARG cc_start: 0.8935 (mtp85) cc_final: 0.8616 (ttm-80) outliers start: 11 outliers final: 9 residues processed: 206 average time/residue: 0.3223 time to fit residues: 86.0891 Evaluate side-chains 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 G residue 100 VAL 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: 0.6980 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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** ** 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 = 0.3681 r_free = 0.3681 target = 0.086170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059020 restraints weight = 30715.990| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.77 r_work: 0.2843 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11168 Z= 0.164 Angle : 0.628 10.479 16102 Z= 0.360 Chirality : 0.035 0.372 1842 Planarity : 0.005 0.061 1208 Dihedral : 30.600 176.871 3390 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 1.89 % Allowed : 38.77 % Favored : 59.35 % 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: 2.50 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.26 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 113 HIS 0.002 0.000 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.014 0.001 TYR B 98 ARG 0.013 0.001 ARG H 116 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 694) hydrogen bonds : angle 3.04407 ( 1760) covalent geometry : bond 0.00367 (11168) covalent geometry : angle 0.62760 (16102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5355.60 seconds wall clock time: 93 minutes 35.51 seconds (5615.51 seconds total)