Starting phenix.real_space_refine on Fri Sep 11 19:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6m_65696/09_2026/9w6m_65696.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6m_65696/09_2026/9w6m_65696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w6m_65696/09_2026/9w6m_65696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6m_65696/09_2026/9w6m_65696.map" model { file = "/net/cci-nas-00/data/ceres_data/9w6m_65696/09_2026/9w6m_65696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6m_65696/09_2026/9w6m_65696.cif" } resolution = 4.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 256 5.49 5 S 14 5.16 5 C 6137 2.51 5 N 2064 2.21 5 O 2552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11023 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "H" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2639 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "J" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2609 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Time building chain proxies: 2.34, per 1000 atoms: 0.21 Number of scatterers: 11023 At special positions: 0 Unit cell: (118.8, 85.8, 121, 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 14 16.00 P 256 15.00 O 2552 8.00 N 2064 7.00 C 6137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 213.2 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 71.8% alpha, 2.5% beta 126 base pairs and 173 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.717A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.558A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.719A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.860A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.503A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.522A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.533A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.738A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 122 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.773A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.952A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.716A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.503A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 41 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.740A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 120 removed outlier: 4.067A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.975A 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 98 removed outlier: 6.398A 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: 7.925A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.130A 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: 7.275A 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 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.729A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 372 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 173 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1484 1.33 - 1.45: 4232 1.45 - 1.57: 5492 1.57 - 1.69: 510 1.69 - 1.81: 24 Bond restraints: 11742 Sorted by residual: bond pdb=" N VAL D 48 " pdb=" CA VAL D 48 " ideal model delta sigma weight residual 1.452 1.496 -0.043 1.18e-02 7.18e+03 1.35e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC I -11 " pdb=" C2' DC I -11 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.97e+00 bond pdb=" C3' DA I 28 " pdb=" C2' DA I 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 bond pdb=" C3' DG I 2 " pdb=" C2' DG I 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.54e+00 ... (remaining 11737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 15146 1.03 - 2.05: 1355 2.05 - 3.08: 437 3.08 - 4.10: 14 4.10 - 5.13: 6 Bond angle restraints: 16958 Sorted by residual: angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4' DG J 27 " pdb=" C4' DG J 27 " pdb=" C3' DG J 27 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 ... (remaining 16953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4599 17.73 - 35.46: 756 35.46 - 53.19: 750 53.19 - 70.92: 250 70.92 - 88.65: 23 Dihedral angle restraints: 6378 sinusoidal: 4272 harmonic: 2106 Sorted by residual: dihedral pdb=" CA ARG F 19 " pdb=" CB ARG F 19 " pdb=" CG ARG F 19 " pdb=" CD ARG F 19 " ideal model delta sinusoidal sigma weight residual 180.00 131.58 48.42 3 1.50e+01 4.44e-03 8.64e+00 dihedral pdb=" N PHE C 25 " pdb=" CA PHE C 25 " pdb=" CB PHE C 25 " pdb=" CG PHE C 25 " ideal model delta sinusoidal sigma weight residual -60.00 -103.51 43.51 3 1.50e+01 4.44e-03 7.82e+00 dihedral pdb=" CA LYS H 108 " pdb=" CB LYS H 108 " pdb=" CG LYS H 108 " pdb=" CD LYS H 108 " ideal model delta sinusoidal sigma weight residual 60.00 102.60 -42.60 3 1.50e+01 4.44e-03 7.65e+00 ... (remaining 6375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1280 0.036 - 0.072: 484 0.072 - 0.109: 149 0.109 - 0.145: 19 0.145 - 0.181: 2 Chirality restraints: 1934 Sorted by residual: chirality pdb=" CA PHE A 78 " pdb=" N PHE A 78 " pdb=" C PHE A 78 " pdb=" CB PHE A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA VAL D 48 " pdb=" N VAL D 48 " pdb=" C VAL D 48 " pdb=" CB VAL D 48 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 1931 not shown) Planarity restraints: 1257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 49 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO D 50 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 77 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ASP A 77 " 0.027 2.00e-02 2.50e+03 pdb=" O ASP A 77 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 78 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -32 " -0.008 2.00e-02 2.50e+03 9.72e-03 2.36e+00 pdb=" N1 DT I -32 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DT I -32 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DT I -32 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT I -32 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I -32 " 0.022 2.00e-02 2.50e+03 pdb=" O4 DT I -32 " -0.015 2.00e-02 2.50e+03 pdb=" C5 DT I -32 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I -32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT I -32 " -0.000 2.00e-02 2.50e+03 ... (remaining 1254 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1452 2.76 - 3.29: 9842 3.29 - 3.83: 21326 3.83 - 4.36: 23083 4.36 - 4.90: 34815 Nonbonded interactions: 90518 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.262 3.040 nonbonded pdb=" O ASN H 63 " pdb=" ND2 ASN H 67 " model vdw 2.306 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.309 3.040 nonbonded pdb=" O LEU G 85 " pdb=" ND2 ASN G 89 " model vdw 2.315 3.120 ... (remaining 90513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 18 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 36 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4930 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 : 0.005 0.043 11742 Z= 0.497 Angle : 0.661 5.130 16958 Z= 0.628 Chirality : 0.041 0.181 1934 Planarity : 0.003 0.042 1257 Dihedral : 25.117 88.650 5022 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.32), residues: 712 helix: 3.29 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -0.23 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 72 TYR 0.006 0.001 TYR D 83 PHE 0.009 0.001 PHE A 78 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.50 (11742) covalent geometry : angle 0.66099 / 0.63 (16958) hydrogen bonds : bond 0.10414 / 7.73 ( 700) hydrogen bonds : angle 2.98099 / 2.11 ( 1763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9270 (mt) cc_final: 0.9031 (mt) REVERT: B 27 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7792 (tm-30) REVERT: B 39 ARG cc_start: 0.7492 (mmt180) cc_final: 0.6755 (mmp-170) REVERT: B 68 ASP cc_start: 0.7922 (m-30) cc_final: 0.7650 (t0) REVERT: B 75 HIS cc_start: -0.0312 (t70) cc_final: -0.0554 (t70) REVERT: B 97 LEU cc_start: 0.6027 (tp) cc_final: 0.4944 (tt) REVERT: C 43 VAL cc_start: 0.7611 (t) cc_final: 0.6656 (t) REVERT: C 97 LEU cc_start: 0.6274 (mt) cc_final: 0.5386 (mt) REVERT: C 108 LEU cc_start: 0.6592 (tp) cc_final: 0.6366 (tp) REVERT: D 52 THR cc_start: -0.3548 (m) cc_final: -0.3773 (p) REVERT: D 61 ILE cc_start: 0.8123 (mt) cc_final: 0.7860 (mt) REVERT: D 100 LEU cc_start: 0.2494 (mt) cc_final: 0.2250 (mt) REVERT: E 67 PHE cc_start: 0.8913 (t80) cc_final: 0.8346 (t80) REVERT: E 73 GLU cc_start: 0.8591 (tt0) cc_final: 0.7963 (pt0) REVERT: E 74 ILE cc_start: 0.7252 (mm) cc_final: 0.6447 (mm) REVERT: E 94 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8268 (mm-30) REVERT: E 107 THR cc_start: 0.7838 (m) cc_final: 0.7337 (m) REVERT: G 102 ILE cc_start: 0.5583 (mt) cc_final: 0.2669 (mm) REVERT: H 40 TYR cc_start: 0.7590 (m-80) cc_final: 0.7030 (m-80) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.1407 time to fit residues: 70.6442 Evaluate side-chains 251 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 39 HIS E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.061874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.048957 restraints weight = 89616.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.051140 restraints weight = 47562.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.052769 restraints weight = 30537.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053917 restraints weight = 21887.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.054707 restraints weight = 16953.767| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11742 Z= 0.179 Angle : 0.657 9.660 16958 Z= 0.395 Chirality : 0.044 0.212 1934 Planarity : 0.007 0.103 1257 Dihedral : 29.207 83.349 3589 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.31), residues: 712 helix: 2.15 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.44 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 131 TYR 0.031 0.002 TYR F 88 PHE 0.023 0.002 PHE A 78 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (11742) covalent geometry : angle 0.65691 / 0.39 (16958) hydrogen bonds : bond 0.05661 / 3.93 ( 700) hydrogen bonds : angle 3.09364 / 2.16 ( 1763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.7561 (mt0) cc_final: 0.7118 (mm-40) REVERT: A 78 PHE cc_start: 0.1284 (m-10) cc_final: 0.0947 (m-10) REVERT: A 82 LEU cc_start: 0.4525 (pt) cc_final: 0.4290 (pt) REVERT: A 106 ASP cc_start: 0.8928 (m-30) cc_final: 0.8715 (m-30) REVERT: B 27 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8111 (tm-30) REVERT: B 34 ILE cc_start: 0.9132 (mt) cc_final: 0.8885 (mt) REVERT: C 23 LEU cc_start: 0.1915 (mm) cc_final: 0.1696 (mm) REVERT: C 43 VAL cc_start: 0.8952 (t) cc_final: 0.8730 (m) REVERT: E 60 LEU cc_start: 0.7339 (mt) cc_final: 0.7127 (tp) REVERT: E 73 GLU cc_start: 0.8032 (tt0) cc_final: 0.7788 (pt0) REVERT: E 74 ILE cc_start: 0.7984 (mm) cc_final: 0.7491 (mt) REVERT: E 124 ILE cc_start: 0.7981 (mp) cc_final: 0.7768 (mp) REVERT: F 25 ASN cc_start: 0.5536 (m110) cc_final: 0.4941 (m-40) REVERT: F 81 VAL cc_start: 0.7624 (t) cc_final: 0.7399 (p) REVERT: F 98 TYR cc_start: 0.6634 (m-10) cc_final: 0.5990 (m-10) REVERT: G 50 TYR cc_start: 0.6728 (t80) cc_final: 0.6361 (t80) REVERT: G 102 ILE cc_start: 0.5602 (mt) cc_final: 0.5387 (mm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1200 time to fit residues: 49.5743 Evaluate side-chains 236 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.045891 restraints weight = 97048.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047265 restraints weight = 57635.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.048230 restraints weight = 40039.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.048909 restraints weight = 30594.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.049449 restraints weight = 25051.178| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11742 Z= 0.240 Angle : 0.737 10.218 16958 Z= 0.425 Chirality : 0.044 0.249 1934 Planarity : 0.008 0.131 1257 Dihedral : 29.830 87.122 3589 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.31), residues: 712 helix: 1.52 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -0.61 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 39 TYR 0.034 0.003 TYR H 40 PHE 0.029 0.003 PHE A 104 HIS 0.009 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.24 (11742) covalent geometry : angle 0.73721 / 0.42 (16958) hydrogen bonds : bond 0.10194 / 6.91 ( 700) hydrogen bonds : angle 3.49609 / 2.44 ( 1763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9587 (tt0) cc_final: 0.9078 (tt0) REVERT: A 54 TYR cc_start: 0.8605 (m-10) cc_final: 0.7898 (m-80) REVERT: A 62 ILE cc_start: 0.8573 (mp) cc_final: 0.8315 (mp) REVERT: A 90 MET cc_start: 0.9359 (mmm) cc_final: 0.9055 (mmm) REVERT: B 27 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8061 (tm-30) REVERT: B 39 ARG cc_start: 0.7899 (mmp-170) cc_final: 0.7201 (mmm160) REVERT: C 23 LEU cc_start: 0.7433 (mm) cc_final: 0.7197 (mm) REVERT: D 52 THR cc_start: 0.6430 (p) cc_final: 0.5873 (p) REVERT: D 65 PHE cc_start: 0.9255 (t80) cc_final: 0.8993 (t80) REVERT: D 68 ASP cc_start: 0.9439 (m-30) cc_final: 0.9194 (m-30) REVERT: D 93 GLU cc_start: 0.9235 (mp0) cc_final: 0.8979 (mp0) REVERT: E 74 ILE cc_start: 0.9082 (mm) cc_final: 0.8791 (mt) REVERT: E 90 MET cc_start: 0.8748 (mpp) cc_final: 0.8440 (mtm) REVERT: E 129 ARG cc_start: 0.9588 (mmm-85) cc_final: 0.9383 (mmm-85) REVERT: F 25 ASN cc_start: 0.6755 (m110) cc_final: 0.6158 (m-40) REVERT: F 39 ARG cc_start: 0.8570 (mpp-170) cc_final: 0.8171 (mmt180) REVERT: F 63 GLU cc_start: 0.9397 (pt0) cc_final: 0.9017 (tm-30) REVERT: F 67 ARG cc_start: 0.9534 (ttp-110) cc_final: 0.8621 (ttp-110) REVERT: F 68 ASP cc_start: 0.8698 (m-30) cc_final: 0.8483 (m-30) REVERT: F 81 VAL cc_start: 0.7901 (t) cc_final: 0.7645 (p) REVERT: F 84 MET cc_start: 0.9018 (tpt) cc_final: 0.8463 (tpp) REVERT: F 97 LEU cc_start: 0.7535 (mp) cc_final: 0.7121 (mp) REVERT: F 98 TYR cc_start: 0.6973 (m-10) cc_final: 0.6508 (m-80) REVERT: G 39 TYR cc_start: 0.7733 (m-80) cc_final: 0.7467 (m-80) REVERT: G 61 GLU cc_start: 0.8930 (tp30) cc_final: 0.8526 (tp30) REVERT: G 65 LEU cc_start: 0.8757 (mt) cc_final: 0.8291 (mt) REVERT: H 120 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8591 (ptmm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1182 time to fit residues: 44.6645 Evaluate side-chains 215 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 30.0000 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.057673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.047834 restraints weight = 90076.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.049310 restraints weight = 53235.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.050295 restraints weight = 36792.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.051080 restraints weight = 28329.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.051639 restraints weight = 22760.953| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11742 Z= 0.163 Angle : 0.643 9.132 16958 Z= 0.378 Chirality : 0.042 0.215 1934 Planarity : 0.005 0.068 1257 Dihedral : 29.970 86.147 3589 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.30), residues: 712 helix: 1.34 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.72 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 39 TYR 0.049 0.003 TYR F 88 PHE 0.027 0.002 PHE C 25 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (11742) covalent geometry : angle 0.64333 / 0.38 (16958) hydrogen bonds : bond 0.05205 / 3.56 ( 700) hydrogen bonds : angle 3.38487 / 2.36 ( 1763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9418 (mmm) cc_final: 0.9124 (mmp) REVERT: A 97 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9144 (mt-10) REVERT: A 104 PHE cc_start: 0.8421 (m-80) cc_final: 0.8157 (m-80) REVERT: A 105 GLU cc_start: 0.9265 (tp30) cc_final: 0.8993 (tp30) REVERT: A 109 LEU cc_start: 0.9290 (mt) cc_final: 0.9077 (mt) REVERT: A 125 GLN cc_start: 0.9424 (mt0) cc_final: 0.9116 (mt0) REVERT: B 39 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7687 (mmp-170) REVERT: B 49 LEU cc_start: 0.8830 (mt) cc_final: 0.8624 (mt) REVERT: B 63 GLU cc_start: 0.9048 (pp20) cc_final: 0.8786 (pp20) REVERT: B 67 ARG cc_start: 0.8881 (ttp-110) cc_final: 0.8373 (ttp-110) REVERT: B 85 ASP cc_start: 0.7881 (m-30) cc_final: 0.7674 (m-30) REVERT: B 90 LEU cc_start: 0.8723 (mm) cc_final: 0.8508 (mt) REVERT: C 23 LEU cc_start: 0.7287 (mm) cc_final: 0.7064 (mm) REVERT: D 45 LEU cc_start: 0.8943 (tp) cc_final: 0.8434 (pp) REVERT: D 68 ASP cc_start: 0.9416 (m-30) cc_final: 0.9136 (m-30) REVERT: D 93 GLU cc_start: 0.9174 (mp0) cc_final: 0.8927 (mp0) REVERT: D 95 GLN cc_start: 0.9151 (pp30) cc_final: 0.8848 (pp30) REVERT: E 68 GLN cc_start: 0.9408 (tp-100) cc_final: 0.9201 (tp-100) REVERT: E 107 THR cc_start: 0.9065 (m) cc_final: 0.8840 (p) REVERT: F 52 GLU cc_start: 0.9339 (mp0) cc_final: 0.8893 (mp0) REVERT: F 53 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8711 (mp0) REVERT: F 63 GLU cc_start: 0.9367 (pt0) cc_final: 0.8964 (tm-30) REVERT: F 67 ARG cc_start: 0.9438 (ttp-110) cc_final: 0.8475 (ttp-110) REVERT: F 68 ASP cc_start: 0.8602 (m-30) cc_final: 0.8385 (m-30) REVERT: F 81 VAL cc_start: 0.7893 (t) cc_final: 0.7650 (p) REVERT: F 84 MET cc_start: 0.8956 (tpt) cc_final: 0.8222 (mmm) REVERT: F 85 ASP cc_start: 0.8223 (m-30) cc_final: 0.7829 (m-30) REVERT: G 61 GLU cc_start: 0.8878 (tp30) cc_final: 0.8479 (tp30) REVERT: G 65 LEU cc_start: 0.8773 (mt) cc_final: 0.8319 (mt) REVERT: H 68 ASP cc_start: 0.9353 (t70) cc_final: 0.9119 (t0) REVERT: H 120 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8584 (ptmm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1171 time to fit residues: 44.8097 Evaluate side-chains 228 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 79 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 89 optimal weight: 40.0000 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.055842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.046401 restraints weight = 93224.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.047785 restraints weight = 55803.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.048722 restraints weight = 38737.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.049446 restraints weight = 29820.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050004 restraints weight = 24111.117| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11742 Z= 0.165 Angle : 0.626 7.203 16958 Z= 0.370 Chirality : 0.041 0.215 1934 Planarity : 0.005 0.057 1257 Dihedral : 30.021 86.706 3589 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.16 % Allowed : 2.63 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.30), residues: 712 helix: 1.45 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.06 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 39 TYR 0.020 0.002 TYR F 88 PHE 0.032 0.003 PHE C 25 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.17 (11742) covalent geometry : angle 0.62620 / 0.37 (16958) hydrogen bonds : bond 0.06207 / 4.25 ( 700) hydrogen bonds : angle 3.35068 / 2.34 ( 1763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8553 (mp) cc_final: 0.8305 (mp) REVERT: A 90 MET cc_start: 0.9367 (mmm) cc_final: 0.9140 (mmm) REVERT: A 104 PHE cc_start: 0.8568 (m-80) cc_final: 0.8322 (m-80) REVERT: A 125 GLN cc_start: 0.9428 (mt0) cc_final: 0.9137 (mt0) REVERT: B 39 ARG cc_start: 0.7952 (mmp-170) cc_final: 0.7737 (mmp-170) REVERT: B 53 GLU cc_start: 0.9253 (mp0) cc_final: 0.9037 (mp0) REVERT: B 63 GLU cc_start: 0.9051 (pp20) cc_final: 0.8815 (pp20) REVERT: B 67 ARG cc_start: 0.8871 (ttp-110) cc_final: 0.8342 (ttp-110) REVERT: B 98 TYR cc_start: 0.6498 (m-10) cc_final: 0.6296 (m-10) REVERT: C 23 LEU cc_start: 0.7452 (mm) cc_final: 0.7203 (mm) REVERT: C 101 THR cc_start: 0.9242 (p) cc_final: 0.8950 (p) REVERT: D 93 GLU cc_start: 0.9234 (mp0) cc_final: 0.8914 (mp0) REVERT: E 68 GLN cc_start: 0.9425 (tp-100) cc_final: 0.9186 (tp-100) REVERT: E 107 THR cc_start: 0.9092 (m) cc_final: 0.8863 (p) REVERT: F 52 GLU cc_start: 0.9306 (mp0) cc_final: 0.9018 (mp0) REVERT: F 53 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8662 (mt-10) REVERT: F 63 GLU cc_start: 0.9366 (pt0) cc_final: 0.9120 (tm-30) REVERT: F 81 VAL cc_start: 0.7789 (t) cc_final: 0.7503 (p) REVERT: F 84 MET cc_start: 0.8982 (tpt) cc_final: 0.8156 (mmm) REVERT: F 85 ASP cc_start: 0.8032 (m-30) cc_final: 0.7765 (m-30) REVERT: F 88 TYR cc_start: 0.8361 (m-80) cc_final: 0.7777 (m-80) REVERT: G 61 GLU cc_start: 0.8896 (tp30) cc_final: 0.8515 (tp30) REVERT: G 65 LEU cc_start: 0.8731 (mt) cc_final: 0.8274 (mt) REVERT: G 72 ASP cc_start: 0.8279 (t70) cc_final: 0.7926 (m-30) REVERT: H 68 ASP cc_start: 0.9336 (t70) cc_final: 0.8884 (t0) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1046 time to fit residues: 39.6474 Evaluate side-chains 222 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046335 restraints weight = 91373.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.047749 restraints weight = 54440.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.048782 restraints weight = 37727.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.049442 restraints weight = 28625.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.050005 restraints weight = 23470.087| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11742 Z= 0.153 Angle : 0.617 7.976 16958 Z= 0.366 Chirality : 0.040 0.213 1934 Planarity : 0.005 0.050 1257 Dihedral : 30.098 86.975 3589 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.16 % Allowed : 2.63 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.30), residues: 712 helix: 1.38 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -0.99 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 39 TYR 0.022 0.002 TYR H 40 PHE 0.033 0.003 PHE C 25 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (11742) covalent geometry : angle 0.61693 / 0.37 (16958) hydrogen bonds : bond 0.05199 / 3.57 ( 700) hydrogen bonds : angle 3.39891 / 2.39 ( 1763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8621 (mp) cc_final: 0.8389 (mp) REVERT: A 90 MET cc_start: 0.9370 (mmm) cc_final: 0.9157 (mmm) REVERT: A 104 PHE cc_start: 0.8532 (m-80) cc_final: 0.8271 (m-80) REVERT: B 27 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7495 (tm-30) REVERT: B 53 GLU cc_start: 0.9243 (mp0) cc_final: 0.9004 (mp0) REVERT: B 67 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8317 (ttp-110) REVERT: C 23 LEU cc_start: 0.7428 (mm) cc_final: 0.7197 (mm) REVERT: C 25 PHE cc_start: 0.7317 (m-80) cc_final: 0.7026 (m-80) REVERT: D 69 ILE cc_start: 0.9293 (mm) cc_final: 0.9090 (pt) REVERT: D 93 GLU cc_start: 0.9203 (mp0) cc_final: 0.8923 (mp0) REVERT: E 68 GLN cc_start: 0.9416 (tp-100) cc_final: 0.9164 (tp-100) REVERT: E 107 THR cc_start: 0.9116 (m) cc_final: 0.8869 (p) REVERT: F 52 GLU cc_start: 0.9284 (mp0) cc_final: 0.9051 (mp0) REVERT: F 53 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8739 (mt-10) REVERT: F 63 GLU cc_start: 0.9358 (pt0) cc_final: 0.9099 (tm-30) REVERT: F 84 MET cc_start: 0.8938 (tpt) cc_final: 0.8145 (mmm) REVERT: F 85 ASP cc_start: 0.8103 (m-30) cc_final: 0.7551 (m-30) REVERT: G 56 GLU cc_start: 0.9064 (pt0) cc_final: 0.8816 (pt0) REVERT: G 61 GLU cc_start: 0.8888 (tp30) cc_final: 0.8496 (tp30) REVERT: G 65 LEU cc_start: 0.8715 (mt) cc_final: 0.8253 (mt) REVERT: G 72 ASP cc_start: 0.8215 (t70) cc_final: 0.7918 (m-30) REVERT: H 43 LYS cc_start: 0.7392 (tptp) cc_final: 0.7114 (tptp) REVERT: H 69 ILE cc_start: 0.9412 (mm) cc_final: 0.9180 (mm) REVERT: H 120 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8647 (ptmm) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.1098 time to fit residues: 40.8766 Evaluate side-chains 220 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 43 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 69 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 24 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046416 restraints weight = 93341.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047818 restraints weight = 55576.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048778 restraints weight = 38291.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.049525 restraints weight = 29166.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.049999 restraints weight = 23387.623| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11742 Z= 0.155 Angle : 0.640 7.883 16958 Z= 0.379 Chirality : 0.041 0.210 1934 Planarity : 0.005 0.055 1257 Dihedral : 30.086 86.904 3589 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.33 % Allowed : 3.62 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 712 helix: 1.23 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.10 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 72 TYR 0.020 0.002 TYR B 51 PHE 0.025 0.002 PHE C 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (11742) covalent geometry : angle 0.63953 / 0.38 (16958) hydrogen bonds : bond 0.04991 / 3.45 ( 700) hydrogen bonds : angle 3.41232 / 2.41 ( 1763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9307 (mmm) cc_final: 0.9058 (mmp) REVERT: A 104 PHE cc_start: 0.8589 (m-80) cc_final: 0.8347 (m-80) REVERT: B 27 GLN cc_start: 0.8613 (mm-40) cc_final: 0.7520 (tm-30) REVERT: B 53 GLU cc_start: 0.9299 (mp0) cc_final: 0.9038 (mp0) REVERT: B 63 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9116 (pp20) REVERT: B 67 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8414 (ttp-110) REVERT: B 88 TYR cc_start: 0.8034 (m-80) cc_final: 0.7712 (m-80) REVERT: B 96 THR cc_start: 0.7805 (m) cc_final: 0.7536 (m) REVERT: B 98 TYR cc_start: 0.6514 (m-10) cc_final: 0.6291 (m-80) REVERT: C 23 LEU cc_start: 0.7367 (mm) cc_final: 0.7109 (mm) REVERT: C 25 PHE cc_start: 0.7483 (m-80) cc_final: 0.7221 (m-80) REVERT: D 72 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8643 (ptm160) REVERT: D 93 GLU cc_start: 0.9189 (mp0) cc_final: 0.8922 (mp0) REVERT: D 95 GLN cc_start: 0.9307 (pp30) cc_final: 0.8854 (pp30) REVERT: E 50 GLU cc_start: 0.9540 (tp30) cc_final: 0.9293 (tp30) REVERT: E 68 GLN cc_start: 0.9410 (tp-100) cc_final: 0.9161 (tp-100) REVERT: E 70 LEU cc_start: 0.8977 (mm) cc_final: 0.8776 (mm) REVERT: E 119 ILE cc_start: 0.8880 (pt) cc_final: 0.8428 (tp) REVERT: E 124 ILE cc_start: 0.9297 (mp) cc_final: 0.9091 (mp) REVERT: F 52 GLU cc_start: 0.9256 (mp0) cc_final: 0.9033 (mp0) REVERT: F 53 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8656 (mt-10) REVERT: F 67 ARG cc_start: 0.9399 (ttp-110) cc_final: 0.9171 (ttp-110) REVERT: F 84 MET cc_start: 0.8934 (tpt) cc_final: 0.8125 (mmm) REVERT: F 85 ASP cc_start: 0.8088 (m-30) cc_final: 0.7527 (m-30) REVERT: G 56 GLU cc_start: 0.9068 (pt0) cc_final: 0.8864 (pt0) REVERT: G 61 GLU cc_start: 0.8945 (tp30) cc_final: 0.8571 (tp30) REVERT: G 65 LEU cc_start: 0.8696 (mt) cc_final: 0.8278 (mt) REVERT: G 72 ASP cc_start: 0.8279 (t70) cc_final: 0.7994 (m-30) REVERT: H 120 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8664 (ptmm) outliers start: 2 outliers final: 1 residues processed: 273 average time/residue: 0.1064 time to fit residues: 39.8213 Evaluate side-chains 224 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 84 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.055091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.046033 restraints weight = 98426.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.047297 restraints weight = 60028.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.048116 restraints weight = 42161.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.048810 restraints weight = 32840.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.049236 restraints weight = 26706.173| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11742 Z= 0.158 Angle : 0.659 11.475 16958 Z= 0.385 Chirality : 0.041 0.210 1934 Planarity : 0.006 0.097 1257 Dihedral : 30.117 87.752 3589 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.16 % Allowed : 0.99 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 712 helix: 1.16 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.15 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 39 TYR 0.027 0.002 TYR C 57 PHE 0.023 0.002 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (11742) covalent geometry : angle 0.65909 / 0.39 (16958) hydrogen bonds : bond 0.05314 / 3.65 ( 700) hydrogen bonds : angle 3.52258 / 2.50 ( 1763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9502 (mm) cc_final: 0.9296 (mm) REVERT: A 104 PHE cc_start: 0.8691 (m-80) cc_final: 0.8417 (m-80) REVERT: B 39 ARG cc_start: 0.7948 (mmp-170) cc_final: 0.7423 (mmm160) REVERT: B 53 GLU cc_start: 0.9259 (mp0) cc_final: 0.8979 (mp0) REVERT: B 63 GLU cc_start: 0.9386 (tm-30) cc_final: 0.9091 (pp20) REVERT: B 67 ARG cc_start: 0.8782 (ttp-110) cc_final: 0.8280 (ttp-110) REVERT: B 88 TYR cc_start: 0.8086 (m-80) cc_final: 0.7791 (m-80) REVERT: B 96 THR cc_start: 0.7925 (m) cc_final: 0.7507 (t) REVERT: C 23 LEU cc_start: 0.7375 (mm) cc_final: 0.7112 (mm) REVERT: C 25 PHE cc_start: 0.7490 (m-80) cc_final: 0.7237 (m-80) REVERT: D 72 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8671 (ptm160) REVERT: D 93 GLU cc_start: 0.9123 (mp0) cc_final: 0.8830 (mp0) REVERT: E 68 GLN cc_start: 0.9426 (tp-100) cc_final: 0.9160 (tp-100) REVERT: F 52 GLU cc_start: 0.9244 (mp0) cc_final: 0.9031 (mp0) REVERT: F 67 ARG cc_start: 0.9403 (ttp-110) cc_final: 0.9178 (ttp-110) REVERT: F 84 MET cc_start: 0.8978 (tpt) cc_final: 0.7259 (mmm) REVERT: F 85 ASP cc_start: 0.8171 (m-30) cc_final: 0.7647 (m-30) REVERT: F 88 TYR cc_start: 0.8146 (m-80) cc_final: 0.6815 (m-10) REVERT: G 56 GLU cc_start: 0.9254 (pt0) cc_final: 0.8840 (pt0) REVERT: G 61 GLU cc_start: 0.8989 (tp30) cc_final: 0.8627 (tp30) REVERT: G 65 LEU cc_start: 0.8748 (mt) cc_final: 0.8296 (mt) REVERT: G 72 ASP cc_start: 0.8313 (t70) cc_final: 0.8003 (m-30) REVERT: H 120 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8648 (ptmm) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.1031 time to fit residues: 37.8173 Evaluate side-chains 222 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042273 restraints weight = 101870.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.044152 restraints weight = 54661.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045460 restraints weight = 35656.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.046382 restraints weight = 25999.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047035 restraints weight = 20448.258| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11742 Z= 0.176 Angle : 0.669 10.358 16958 Z= 0.392 Chirality : 0.042 0.220 1934 Planarity : 0.006 0.078 1257 Dihedral : 30.301 89.296 3589 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.16 % Allowed : 0.66 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.30), residues: 712 helix: 0.96 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.25 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 39 TYR 0.021 0.003 TYR A 54 PHE 0.023 0.002 PHE D 65 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 (11742) covalent geometry : angle 0.66923 / 0.39 (16958) hydrogen bonds : bond 0.06701 / 4.56 ( 700) hydrogen bonds : angle 3.62600 / 2.57 ( 1763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8704 (t80) cc_final: 0.8345 (t80) REVERT: A 124 ILE cc_start: 0.8444 (mp) cc_final: 0.8226 (mp) REVERT: B 37 LEU cc_start: 0.8592 (mm) cc_final: 0.8235 (mm) REVERT: C 25 PHE cc_start: 0.6746 (m-80) cc_final: 0.6465 (m-80) REVERT: E 124 ILE cc_start: 0.7849 (mp) cc_final: 0.7445 (mp) REVERT: F 53 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7764 (mt-10) REVERT: F 67 ARG cc_start: 0.9522 (ttp-110) cc_final: 0.9112 (ttp-110) REVERT: F 84 MET cc_start: 0.9021 (tpt) cc_final: 0.8742 (tpp) REVERT: G 56 GLU cc_start: 0.8803 (pt0) cc_final: 0.8488 (pt0) REVERT: G 72 ASP cc_start: 0.8443 (t70) cc_final: 0.8123 (m-30) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.1030 time to fit residues: 37.5013 Evaluate side-chains 218 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 89 optimal weight: 40.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.054614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.042899 restraints weight = 100760.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.044796 restraints weight = 53285.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.046154 restraints weight = 34581.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.047115 restraints weight = 25025.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.047783 restraints weight = 19589.614| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11742 Z= 0.157 Angle : 0.688 12.228 16958 Z= 0.398 Chirality : 0.042 0.278 1934 Planarity : 0.006 0.073 1257 Dihedral : 30.279 89.749 3589 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.16 % Allowed : 0.82 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.30), residues: 712 helix: 0.90 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.23 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 72 TYR 0.025 0.002 TYR F 88 PHE 0.032 0.003 PHE A 104 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (11742) covalent geometry : angle 0.68839 / 0.40 (16958) hydrogen bonds : bond 0.04883 / 3.33 ( 700) hydrogen bonds : angle 3.61948 / 2.58 ( 1763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8703 (t80) cc_final: 0.8358 (t80) REVERT: B 37 LEU cc_start: 0.8578 (mm) cc_final: 0.8213 (mm) REVERT: C 23 LEU cc_start: 0.2648 (mm) cc_final: 0.2416 (mm) REVERT: C 25 PHE cc_start: 0.6727 (m-80) cc_final: 0.6464 (m-80) REVERT: E 124 ILE cc_start: 0.7773 (mp) cc_final: 0.7336 (mp) REVERT: F 53 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7698 (mt-10) REVERT: F 84 MET cc_start: 0.8903 (tpt) cc_final: 0.8413 (tpp) REVERT: G 56 GLU cc_start: 0.8866 (pt0) cc_final: 0.8573 (pt0) REVERT: G 72 ASP cc_start: 0.8434 (t70) cc_final: 0.8108 (m-30) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.1036 time to fit residues: 38.3245 Evaluate side-chains 223 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.041674 restraints weight = 101453.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.043507 restraints weight = 54128.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044826 restraints weight = 35297.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045739 restraints weight = 25756.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.046403 restraints weight = 20354.665| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11742 Z= 0.181 Angle : 0.713 10.816 16958 Z= 0.416 Chirality : 0.042 0.219 1934 Planarity : 0.005 0.065 1257 Dihedral : 30.309 87.916 3589 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.30), residues: 712 helix: 0.66 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.38 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 39 TYR 0.030 0.003 TYR F 88 PHE 0.035 0.003 PHE D 65 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (11742) covalent geometry : angle 0.71344 / 0.42 (16958) hydrogen bonds : bond 0.06723 / 4.57 ( 700) hydrogen bonds : angle 3.73625 / 2.65 ( 1763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1735.01 seconds wall clock time: 30 minutes 41.93 seconds (1841.93 seconds total)