Starting phenix.real_space_refine on Sat Nov 16 02:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcd_36158/11_2024/8jcd_36158.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcd_36158/11_2024/8jcd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcd_36158/11_2024/8jcd_36158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcd_36158/11_2024/8jcd_36158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcd_36158/11_2024/8jcd_36158.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcd_36158/11_2024/8jcd_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-5513/modules/chem_data/mon_lib" Total number of atoms: 10506 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "E" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 752 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "H" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "I" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2476 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Chain: "J" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2444 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Time building chain proxies: 6.40, per 1000 atoms: 0.61 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: 3.17 Conformation dependent library (CDL) restraints added in 803.9 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: 5.38 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: 3.95 Time building geometry restraints manager: 3.46 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: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.120 Process input model: 31.080 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11168 Z= 0.190 Angle : 0.574 10.776 16102 Z= 0.333 Chirality : 0.035 0.225 1842 Planarity : 0.004 0.042 1208 Dihedral : 28.678 178.870 4774 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 0.69 % Allowed : 35.68 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.32), residues: 688 helix: 1.93 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.014 0.001 PHE C 25 TYR 0.026 0.001 TYR D 61 ARG 0.009 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.906 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: 0.3455 time to fit residues: 101.9019 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 : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11168 Z= 0.294 Angle : 0.600 7.715 16102 Z= 0.352 Chirality : 0.036 0.173 1842 Planarity : 0.004 0.041 1208 Dihedral : 30.550 178.835 3392 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 4.12 % Allowed : 34.82 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.33), residues: 688 helix: 2.22 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -1.32 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.010 0.001 PHE C 25 TYR 0.019 0.002 TYR D 61 ARG 0.006 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7791 (tm-30) REVERT: A 59 GLU cc_start: 0.8527 (pm20) cc_final: 0.8093 (pm20) REVERT: A 133 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8381 (tt0) REVERT: B 84 MET cc_start: 0.8457 (tpp) cc_final: 0.8194 (tpp) REVERT: C 24 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8996 (mm110) REVERT: C 38 ASN cc_start: 0.9009 (t0) cc_final: 0.8655 (t0) REVERT: C 56 GLU cc_start: 0.8885 (tt0) cc_final: 0.8510 (tt0) REVERT: C 68 ASN cc_start: 0.9007 (m-40) cc_final: 0.8432 (m-40) REVERT: C 95 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8679 (tppt) REVERT: D 78 GLU cc_start: 0.8786 (mp0) cc_final: 0.8502 (mp0) REVERT: D 127 MET cc_start: 0.8673 (ttm) cc_final: 0.8444 (ttm) REVERT: E 94 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8623 (mm-30) REVERT: F 25 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8495 (t0) REVERT: F 50 ILE cc_start: 0.9391 (mm) cc_final: 0.9174 (mt) REVERT: F 84 MET cc_start: 0.8686 (tpp) cc_final: 0.8346 (tpp) REVERT: F 88 TYR cc_start: 0.9405 (m-80) cc_final: 0.9136 (m-80) REVERT: F 91 LYS cc_start: 0.9344 (ttpt) cc_final: 0.9088 (ttmt) REVERT: G 41 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8751 (mt-10) REVERT: G 81 ARG cc_start: 0.8680 (tpt170) cc_final: 0.8260 (tpt170) REVERT: G 95 LYS cc_start: 0.9351 (ttmt) cc_final: 0.9091 (ttmm) REVERT: G 104 GLN cc_start: 0.8754 (mp10) cc_final: 0.8458 (mp10) REVERT: H 77 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8136 (mtm-85) REVERT: H 85 SER cc_start: 0.9309 (t) cc_final: 0.8889 (t) REVERT: H 89 ASP cc_start: 0.9167 (t70) cc_final: 0.8869 (t0) REVERT: H 141 ARG cc_start: 0.8928 (mtp85) cc_final: 0.8531 (ttm110) outliers start: 24 outliers final: 11 residues processed: 227 average time/residue: 0.3226 time to fit residues: 93.1238 Evaluate side-chains 205 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1565 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= 0.215 Angle : 0.579 8.287 16102 Z= 0.339 Chirality : 0.034 0.209 1842 Planarity : 0.004 0.044 1208 Dihedral : 30.561 178.462 3390 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.91 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: 2.39 (0.33), residues: 688 helix: 2.35 (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 0.006 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.008 0.001 PHE C 25 TYR 0.018 0.001 TYR D 61 ARG 0.006 0.001 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7828 (tm-30) REVERT: A 59 GLU cc_start: 0.8588 (pm20) cc_final: 0.8144 (pm20) REVERT: A 94 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8844 (mm-30) REVERT: A 133 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8330 (tt0) REVERT: B 74 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8822 (mm-30) REVERT: B 84 MET cc_start: 0.8496 (tpp) cc_final: 0.8257 (tpp) REVERT: B 92 ARG cc_start: 0.9263 (ttp80) cc_final: 0.8802 (mmm-85) REVERT: C 24 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8955 (mm110) REVERT: C 38 ASN cc_start: 0.8955 (t0) cc_final: 0.8707 (t0) REVERT: C 56 GLU cc_start: 0.8846 (tt0) cc_final: 0.8427 (tt0) REVERT: C 68 ASN cc_start: 0.8923 (m-40) cc_final: 0.8608 (m-40) REVERT: C 95 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8578 (tppt) REVERT: D 78 GLU cc_start: 0.8803 (mp0) cc_final: 0.8514 (mp0) REVERT: D 127 MET cc_start: 0.8732 (ttm) cc_final: 0.8530 (ttm) REVERT: D 137 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8663 (mtmm) REVERT: E 94 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8632 (mm-30) REVERT: F 25 ASN cc_start: 0.9170 (m-40) cc_final: 0.8503 (t0) REVERT: F 84 MET cc_start: 0.8722 (tpp) cc_final: 0.8372 (tpp) REVERT: F 88 TYR cc_start: 0.9416 (m-10) cc_final: 0.9166 (m-80) REVERT: F 91 LYS cc_start: 0.9324 (ttpt) cc_final: 0.9048 (ttmt) REVERT: G 41 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8715 (mt-10) REVERT: G 81 ARG cc_start: 0.8650 (tpt170) cc_final: 0.8282 (tpt170) REVERT: G 95 LYS cc_start: 0.9348 (ttmt) cc_final: 0.9083 (ttmm) REVERT: G 104 GLN cc_start: 0.8809 (mp10) cc_final: 0.8518 (mp10) REVERT: H 77 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8151 (mtm-85) REVERT: H 85 SER cc_start: 0.9219 (t) cc_final: 0.8948 (t) REVERT: H 89 ASP cc_start: 0.9103 (t70) cc_final: 0.8687 (t0) REVERT: H 141 ARG cc_start: 0.8921 (mtp85) cc_final: 0.8532 (ttm110) outliers start: 21 outliers final: 10 residues processed: 220 average time/residue: 0.3280 time to fit residues: 91.8935 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 : 0.919 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 79 ILE 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 82 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 chunk 83 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1874 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= 0.179 Angle : 0.564 8.953 16102 Z= 0.332 Chirality : 0.034 0.240 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.507 178.002 3390 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 3.95 % Allowed : 33.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.32), residues: 688 helix: 2.41 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 113 HIS 0.002 0.000 HIS E 113 PHE 0.007 0.001 PHE B 100 TYR 0.017 0.001 TYR D 61 ARG 0.006 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7833 (tm-30) REVERT: A 59 GLU cc_start: 0.8635 (pm20) cc_final: 0.8187 (pm20) REVERT: A 94 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8742 (mm-30) REVERT: A 133 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8305 (tt0) REVERT: B 74 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8903 (mm-30) REVERT: B 84 MET cc_start: 0.8468 (tpp) cc_final: 0.8263 (tpp) REVERT: B 92 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8754 (mmm-85) REVERT: B 98 TYR cc_start: 0.8313 (m-80) cc_final: 0.8064 (m-80) REVERT: C 24 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8891 (mm110) REVERT: C 56 GLU cc_start: 0.8808 (tt0) cc_final: 0.8333 (tt0) REVERT: C 68 ASN cc_start: 0.8826 (m-40) cc_final: 0.8567 (m-40) REVERT: C 95 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8607 (tppt) REVERT: D 78 GLU cc_start: 0.8829 (mp0) cc_final: 0.8570 (mp0) REVERT: D 127 MET cc_start: 0.8639 (ttm) cc_final: 0.8360 (ttm) REVERT: E 133 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: F 25 ASN cc_start: 0.9136 (m-40) cc_final: 0.8525 (t0) REVERT: F 84 MET cc_start: 0.8687 (tpp) cc_final: 0.8357 (tpp) REVERT: F 88 TYR cc_start: 0.9379 (m-10) cc_final: 0.9150 (m-80) REVERT: F 91 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8997 (ttmt) REVERT: G 71 ARG cc_start: 0.9173 (mmm-85) cc_final: 0.8899 (mmm-85) REVERT: G 81 ARG cc_start: 0.8641 (tpt170) cc_final: 0.8283 (tpt170) REVERT: G 95 LYS cc_start: 0.9353 (ttmt) cc_final: 0.9088 (ttmm) REVERT: G 104 GLN cc_start: 0.8844 (mp10) cc_final: 0.8566 (mp10) REVERT: H 77 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.8129 (mtm-85) REVERT: H 85 SER cc_start: 0.9157 (t) cc_final: 0.8865 (t) REVERT: H 89 ASP cc_start: 0.9091 (t70) cc_final: 0.8656 (t0) REVERT: H 141 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8681 (ttm-80) outliers start: 23 outliers final: 12 residues processed: 229 average time/residue: 0.3126 time to fit residues: 91.5475 Evaluate side-chains 212 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 66 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11168 Z= 0.265 Angle : 0.601 10.214 16102 Z= 0.349 Chirality : 0.036 0.302 1842 Planarity : 0.004 0.044 1208 Dihedral : 30.709 178.109 3390 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 3.60 % Allowed : 35.16 % 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 (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: 2.53 (0.33), residues: 688 helix: 2.47 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.33 (0.46), 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 0.009 0.001 PHE C 25 TYR 0.019 0.001 TYR D 61 ARG 0.007 0.000 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7831 (tm-30) REVERT: A 59 GLU cc_start: 0.8709 (pm20) cc_final: 0.8273 (pm20) REVERT: A 94 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8719 (mm-30) REVERT: A 133 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8312 (tt0) REVERT: B 74 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8880 (mm-30) REVERT: B 84 MET cc_start: 0.8511 (tpp) cc_final: 0.8301 (tpp) REVERT: C 24 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8961 (mm110) REVERT: C 25 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.7652 (t80) REVERT: C 56 GLU cc_start: 0.8915 (tt0) cc_final: 0.8462 (tt0) REVERT: C 68 ASN cc_start: 0.8857 (m-40) cc_final: 0.8582 (m-40) REVERT: C 95 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8641 (tppt) REVERT: D 78 GLU cc_start: 0.8865 (mp0) cc_final: 0.8582 (mp0) REVERT: D 127 MET cc_start: 0.8602 (ttm) cc_final: 0.8322 (ttm) REVERT: D 137 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8705 (mtmm) REVERT: E 133 GLU cc_start: 0.8804 (pt0) cc_final: 0.8001 (pm20) REVERT: F 25 ASN cc_start: 0.9192 (m-40) cc_final: 0.8511 (t0) REVERT: F 84 MET cc_start: 0.8655 (tpp) cc_final: 0.8324 (tpp) REVERT: F 88 TYR cc_start: 0.9412 (m-10) cc_final: 0.9163 (m-80) REVERT: F 91 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8984 (ttmt) REVERT: G 81 ARG cc_start: 0.8727 (tpt170) cc_final: 0.8358 (tpt170) REVERT: G 95 LYS cc_start: 0.9360 (ttmt) cc_final: 0.9090 (ttmm) REVERT: G 104 GLN cc_start: 0.8841 (mp10) cc_final: 0.8557 (mp10) REVERT: H 77 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8111 (mtm-85) REVERT: H 83 MET cc_start: 0.9311 (tpp) cc_final: 0.8725 (tpp) REVERT: H 85 SER cc_start: 0.9278 (t) cc_final: 0.8968 (t) REVERT: H 89 ASP cc_start: 0.9125 (t70) cc_final: 0.8867 (t0) REVERT: H 116 ARG cc_start: 0.8588 (ttt90) cc_final: 0.7996 (ttt90) REVERT: H 132 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7496 (mt-10) REVERT: H 141 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8544 (ttm110) outliers start: 21 outliers final: 13 residues processed: 216 average time/residue: 0.3278 time to fit residues: 90.2872 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 : 0.913 ------------------------------------------------------------------------------- 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 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 G residue 79 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2196 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= 0.201 Angle : 0.591 10.531 16102 Z= 0.341 Chirality : 0.035 0.304 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.610 177.904 3390 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 3.09 % Allowed : 36.54 % 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 (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: 2.59 (0.33), residues: 688 helix: 2.52 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.32 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.010 0.001 PHE C 25 TYR 0.019 0.001 TYR D 61 ARG 0.007 0.001 ARG D 63 *********************** 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 222 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7857 (tm-30) REVERT: A 59 GLU cc_start: 0.8738 (pm20) cc_final: 0.8298 (pm20) REVERT: A 94 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8704 (mm-30) REVERT: A 133 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8309 (tt0) REVERT: B 74 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8816 (mm-30) REVERT: B 98 TYR cc_start: 0.8368 (m-80) cc_final: 0.7970 (m-80) REVERT: C 24 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8924 (mm110) REVERT: C 56 GLU cc_start: 0.8858 (tt0) cc_final: 0.8359 (tt0) REVERT: C 68 ASN cc_start: 0.8826 (m-40) cc_final: 0.8595 (m-40) REVERT: C 95 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8563 (tppt) REVERT: D 78 GLU cc_start: 0.8902 (mp0) cc_final: 0.8614 (mp0) REVERT: E 133 GLU cc_start: 0.8766 (pt0) cc_final: 0.8051 (pm20) REVERT: F 25 ASN cc_start: 0.9202 (m-40) cc_final: 0.8483 (t0) REVERT: F 53 GLU cc_start: 0.8796 (tp30) cc_final: 0.8556 (tp30) REVERT: F 79 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8057 (mttt) REVERT: F 84 MET cc_start: 0.8640 (tpp) cc_final: 0.8335 (tpp) REVERT: F 88 TYR cc_start: 0.9376 (m-10) cc_final: 0.9144 (m-80) REVERT: F 91 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8903 (ttmt) REVERT: G 71 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8885 (mmm-85) REVERT: G 81 ARG cc_start: 0.8676 (tpt170) cc_final: 0.8331 (tpt170) REVERT: G 95 LYS cc_start: 0.9355 (ttmt) cc_final: 0.9075 (ttmm) REVERT: G 104 GLN cc_start: 0.8865 (mp10) cc_final: 0.8589 (mp10) REVERT: H 77 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8095 (mtm-85) REVERT: H 83 MET cc_start: 0.9214 (tpp) cc_final: 0.8775 (tpp) REVERT: H 85 SER cc_start: 0.9223 (t) cc_final: 0.8876 (t) REVERT: H 89 ASP cc_start: 0.9089 (t70) cc_final: 0.8617 (t0) REVERT: H 116 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8314 (ttt90) REVERT: H 141 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8602 (ttm110) outliers start: 18 outliers final: 13 residues processed: 214 average time/residue: 0.3349 time to fit residues: 91.0543 Evaluate side-chains 209 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 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 F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.0770 chunk 52 optimal weight: 7.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11168 Z= 0.274 Angle : 0.618 8.915 16102 Z= 0.358 Chirality : 0.036 0.342 1842 Planarity : 0.004 0.046 1208 Dihedral : 30.744 177.936 3390 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % 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 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 113 HIS 0.006 0.001 HIS G 31 PHE 0.010 0.001 PHE C 25 TYR 0.021 0.001 TYR D 61 ARG 0.007 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7914 (tm-30) REVERT: A 59 GLU cc_start: 0.8774 (pm20) cc_final: 0.8350 (pm20) REVERT: A 94 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 133 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8358 (tt0) REVERT: B 74 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8818 (mm-30) REVERT: C 24 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8981 (mm110) REVERT: C 25 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.7695 (t80) REVERT: C 56 GLU cc_start: 0.8929 (tt0) cc_final: 0.8468 (tt0) REVERT: C 68 ASN cc_start: 0.8850 (m-40) cc_final: 0.8608 (m-40) REVERT: C 95 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8604 (tppt) REVERT: D 78 GLU cc_start: 0.8897 (mp0) cc_final: 0.8582 (mp0) REVERT: D 137 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8720 (mtmm) REVERT: E 133 GLU cc_start: 0.8777 (pt0) cc_final: 0.8096 (pm20) REVERT: F 25 ASN cc_start: 0.9219 (m-40) cc_final: 0.8547 (t0) REVERT: F 79 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8093 (mttt) REVERT: F 84 MET cc_start: 0.8655 (tpp) cc_final: 0.8336 (tpp) REVERT: F 88 TYR cc_start: 0.9390 (m-10) cc_final: 0.9153 (m-80) REVERT: F 91 LYS cc_start: 0.9174 (ttpt) cc_final: 0.8965 (ttmt) REVERT: G 95 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9114 (ttmm) REVERT: G 104 GLN cc_start: 0.8932 (mp10) cc_final: 0.8644 (mp10) REVERT: H 77 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.8077 (mtm-85) REVERT: H 83 MET cc_start: 0.9259 (tpp) cc_final: 0.8798 (tpp) REVERT: H 85 SER cc_start: 0.9307 (t) cc_final: 0.8988 (t) REVERT: H 89 ASP cc_start: 0.9128 (t70) cc_final: 0.8910 (t0) REVERT: H 141 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8547 (ttm110) outliers start: 22 outliers final: 16 residues processed: 210 average time/residue: 0.3191 time to fit residues: 86.2262 Evaluate side-chains 208 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 E residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 0.2980 chunk 56 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11168 Z= 0.261 Angle : 0.619 9.095 16102 Z= 0.357 Chirality : 0.036 0.339 1842 Planarity : 0.004 0.046 1208 Dihedral : 30.785 177.546 3390 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.77 % Allowed : 35.68 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.32), residues: 688 helix: 2.48 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.25 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 113 HIS 0.003 0.001 HIS G 31 PHE 0.010 0.001 PHE C 25 TYR 0.022 0.001 TYR D 61 ARG 0.007 0.000 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7867 (tm-30) REVERT: A 59 GLU cc_start: 0.8784 (pm20) cc_final: 0.8314 (pm20) REVERT: A 94 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8629 (mm-30) REVERT: A 133 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8374 (tt0) REVERT: B 74 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8825 (mm-30) REVERT: C 24 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8972 (mm110) REVERT: C 25 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.7682 (t80) REVERT: C 56 GLU cc_start: 0.8937 (tt0) cc_final: 0.8481 (tt0) REVERT: C 68 ASN cc_start: 0.8850 (m-40) cc_final: 0.8612 (m-40) REVERT: C 95 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8638 (tppt) REVERT: D 137 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8745 (mtmm) REVERT: E 133 GLU cc_start: 0.8750 (pt0) cc_final: 0.8068 (pm20) REVERT: F 25 ASN cc_start: 0.9231 (m-40) cc_final: 0.8602 (t0) REVERT: F 79 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8083 (mttt) REVERT: F 84 MET cc_start: 0.8640 (tpp) cc_final: 0.8323 (tpp) REVERT: F 88 TYR cc_start: 0.9408 (m-10) cc_final: 0.9160 (m-80) REVERT: F 91 LYS cc_start: 0.9191 (ttpt) cc_final: 0.8985 (ttmt) REVERT: G 38 ASN cc_start: 0.9438 (t0) cc_final: 0.9209 (t0) REVERT: G 95 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9113 (ttmm) REVERT: G 104 GLN cc_start: 0.8998 (mp10) cc_final: 0.8718 (mp10) REVERT: H 77 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8028 (mtm-85) REVERT: H 83 MET cc_start: 0.9227 (tpp) cc_final: 0.8814 (tpp) REVERT: H 85 SER cc_start: 0.9297 (t) cc_final: 0.8968 (t) REVERT: H 89 ASP cc_start: 0.9116 (t70) cc_final: 0.8885 (t0) REVERT: H 141 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8548 (ttm110) outliers start: 22 outliers final: 16 residues processed: 205 average time/residue: 0.3023 time to fit residues: 80.9481 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 : 0.870 ------------------------------------------------------------------------------- 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 E residue 61 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11168 Z= 0.327 Angle : 0.658 8.911 16102 Z= 0.377 Chirality : 0.038 0.363 1842 Planarity : 0.005 0.046 1208 Dihedral : 30.975 177.434 3390 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 3.26 % Allowed : 36.36 % 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 (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: 2.47 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.32 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE C 25 TYR 0.025 0.002 TYR D 61 ARG 0.009 0.001 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7859 (tm-30) REVERT: A 59 GLU cc_start: 0.8804 (pm20) cc_final: 0.8327 (pm20) REVERT: A 94 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8622 (mm-30) REVERT: A 133 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8377 (tt0) REVERT: B 74 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8875 (mm-30) REVERT: C 25 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7698 (t80) REVERT: C 56 GLU cc_start: 0.8963 (tt0) cc_final: 0.8537 (tt0) REVERT: C 68 ASN cc_start: 0.8878 (m-40) cc_final: 0.8636 (m-40) REVERT: C 95 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8705 (tppt) REVERT: D 137 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8771 (mtmm) REVERT: E 133 GLU cc_start: 0.8746 (pt0) cc_final: 0.8021 (pm20) REVERT: F 25 ASN cc_start: 0.9212 (m-40) cc_final: 0.8810 (t0) REVERT: F 79 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8082 (mttt) REVERT: F 84 MET cc_start: 0.8661 (tpp) cc_final: 0.8360 (tpp) REVERT: F 88 TYR cc_start: 0.9393 (m-10) cc_final: 0.9142 (m-80) REVERT: G 38 ASN cc_start: 0.9435 (t0) cc_final: 0.9201 (t0) REVERT: G 104 GLN cc_start: 0.9093 (mp10) cc_final: 0.8802 (mp10) REVERT: H 77 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8070 (mtm-85) REVERT: H 83 MET cc_start: 0.9270 (tpp) cc_final: 0.8839 (tpp) REVERT: H 85 SER cc_start: 0.9336 (t) cc_final: 0.9008 (t) REVERT: H 89 ASP cc_start: 0.9119 (t70) cc_final: 0.8895 (t0) REVERT: H 132 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7772 (mt-10) REVERT: H 141 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8527 (ttm110) outliers start: 19 outliers final: 15 residues processed: 198 average time/residue: 0.2968 time to fit residues: 76.8487 Evaluate side-chains 201 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 62 LEU 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 74 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11168 Z= 0.271 Angle : 0.640 9.148 16102 Z= 0.368 Chirality : 0.037 0.349 1842 Planarity : 0.005 0.046 1208 Dihedral : 30.924 177.279 3390 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.09 % Allowed : 36.88 % 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 (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: 2.55 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 161 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 0.011 0.001 PHE C 25 TYR 0.025 0.001 TYR D 61 ARG 0.010 0.001 ARG H 116 ********************** 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 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7865 (tm-30) REVERT: A 59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8308 (pm20) REVERT: A 94 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8622 (mm-30) REVERT: A 133 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8378 (tt0) REVERT: B 74 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8838 (mm-30) REVERT: C 24 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8906 (mm-40) REVERT: C 25 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.7682 (t80) REVERT: C 56 GLU cc_start: 0.8938 (tt0) cc_final: 0.8496 (tt0) REVERT: C 68 ASN cc_start: 0.8839 (m-40) cc_final: 0.8624 (m-40) REVERT: C 95 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8710 (tppt) REVERT: D 137 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8750 (mtmm) REVERT: E 73 GLU cc_start: 0.9011 (tt0) cc_final: 0.8726 (tt0) REVERT: E 133 GLU cc_start: 0.8769 (pt0) cc_final: 0.8034 (pm20) REVERT: F 25 ASN cc_start: 0.9211 (m-40) cc_final: 0.8784 (t0) REVERT: F 79 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8080 (mttt) REVERT: F 84 MET cc_start: 0.8647 (tpp) cc_final: 0.8316 (tpp) REVERT: F 88 TYR cc_start: 0.9381 (m-10) cc_final: 0.9147 (m-80) REVERT: G 38 ASN cc_start: 0.9424 (t0) cc_final: 0.9181 (t0) REVERT: G 104 GLN cc_start: 0.9106 (mp10) cc_final: 0.8852 (mp10) REVERT: H 77 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8028 (mtm-85) REVERT: H 83 MET cc_start: 0.9236 (tpp) cc_final: 0.8868 (tpp) REVERT: H 85 SER cc_start: 0.9310 (t) cc_final: 0.8987 (t) REVERT: H 89 ASP cc_start: 0.9112 (t70) cc_final: 0.8872 (t0) REVERT: H 141 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8528 (ttm110) outliers start: 18 outliers final: 16 residues processed: 197 average time/residue: 0.2899 time to fit residues: 74.9477 Evaluate side-chains 200 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 D residue 66 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.084803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057605 restraints weight = 30753.337| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.75 r_work: 0.2816 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11168 Z= 0.207 Angle : 0.628 10.240 16102 Z= 0.360 Chirality : 0.035 0.345 1842 Planarity : 0.004 0.047 1208 Dihedral : 30.731 176.566 3390 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 2.74 % Allowed : 37.39 % Favored : 59.86 % 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: 2.68 (0.32), residues: 688 helix: 2.65 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.33 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 113 HIS 0.002 0.001 HIS E 113 PHE 0.009 0.001 PHE C 25 TYR 0.021 0.001 TYR D 61 ARG 0.009 0.001 ARG H 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2313.26 seconds wall clock time: 42 minutes 27.63 seconds (2547.63 seconds total)