Starting phenix.real_space_refine on Wed May 14 16:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jla_36390/05_2025/8jla_36390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jla_36390/05_2025/8jla_36390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jla_36390/05_2025/8jla_36390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jla_36390/05_2025/8jla_36390.map" model { file = "/net/cci-nas-00/data/ceres_data/8jla_36390/05_2025/8jla_36390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jla_36390/05_2025/8jla_36390.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 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 312 5.49 5 S 14 5.16 5 C 6761 2.51 5 N 2309 2.21 5 O 2918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12314 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: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3200 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3196 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Time building chain proxies: 6.76, per 1000 atoms: 0.55 Number of scatterers: 12314 At special positions: 0 Unit cell: (74.2, 121.9, 129.32, 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 312 15.00 O 2918 8.00 N 2309 7.00 C 6761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 793.9 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.7% alpha, 2.7% beta 156 base pairs and 283 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.557A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.558A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.716A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.528A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.763A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.024A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.545A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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: 3.714A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.481A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.761A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.854A 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 removed outlier: 3.500A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.334A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.765A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.085A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 403 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 401 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 283 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 3.25 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: 2149 1.33 - 1.45: 4573 1.45 - 1.57: 5804 1.57 - 1.69: 622 1.69 - 1.81: 24 Bond restraints: 13172 Sorted by residual: bond pdb=" CZ ARG C 88 " pdb=" NH2 ARG C 88 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.83e+00 bond pdb=" CZ ARG G 88 " pdb=" NH2 ARG G 88 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.58e+00 bond pdb=" CZ ARG B 78 " pdb=" NH2 ARG B 78 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.02e+00 bond pdb=" CZ ARG B 35 " pdb=" NH2 ARG B 35 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.69e+00 bond pdb=" CZ ARG B 67 " pdb=" NH2 ARG B 67 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.09e+00 ... (remaining 13167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 17148 1.42 - 2.84: 1692 2.84 - 4.26: 242 4.26 - 5.68: 37 5.68 - 7.10: 11 Bond angle restraints: 19130 Sorted by residual: angle pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 120.52 124.12 -3.60 8.30e-01 1.45e+00 1.88e+01 angle pdb=" C4' DG J -53 " pdb=" O4' DG J -53 " pdb=" C1' DG J -53 " ideal model delta sigma weight residual 109.70 103.73 5.97 1.50e+00 4.44e-01 1.58e+01 angle pdb=" CD ARG B 35 " pdb=" NE ARG B 35 " pdb=" CZ ARG B 35 " ideal model delta sigma weight residual 124.40 129.76 -5.36 1.40e+00 5.10e-01 1.46e+01 angle pdb=" C GLN E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 120.44 125.22 -4.78 1.30e+00 5.92e-01 1.35e+01 angle pdb=" C4' DC J 37 " pdb=" O4' DC J 37 " pdb=" C1' DC J 37 " ideal model delta sigma weight residual 109.70 104.35 5.35 1.50e+00 4.44e-01 1.27e+01 ... (remaining 19125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 5506 33.00 - 65.99: 1547 65.99 - 98.99: 39 98.99 - 131.98: 0 131.98 - 164.98: 2 Dihedral angle restraints: 7094 sinusoidal: 4936 harmonic: 2158 Sorted by residual: dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 55.02 164.98 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 68.92 151.08 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" C LYS C 74 " pdb=" N LYS C 74 " pdb=" CA LYS C 74 " pdb=" CB LYS C 74 " ideal model delta harmonic sigma weight residual -122.60 -131.76 9.16 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 7091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1830 0.068 - 0.136: 307 0.136 - 0.204: 31 0.204 - 0.272: 5 0.272 - 0.340: 1 Chirality restraints: 2174 Sorted by residual: chirality pdb=" C4' DG J -53 " pdb=" C5' DG J -53 " pdb=" O4' DG J -53 " pdb=" C3' DG J -53 " both_signs ideal model delta sigma weight residual False -2.53 -2.19 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE G 102 " pdb=" N ILE G 102 " pdb=" C ILE G 102 " pdb=" CB ILE G 102 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C4' DC J 37 " pdb=" C5' DC J 37 " pdb=" O4' DC J 37 " pdb=" C3' DC J 37 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2171 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 43 " 0.003 2.00e-02 2.50e+03 2.73e-02 2.05e+01 pdb=" N9 DA I 43 " -0.064 2.00e-02 2.50e+03 pdb=" C8 DA I 43 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DA I 43 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA I 43 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 43 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 43 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 43 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA I 43 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA I 43 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 43 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 42 " -0.059 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR H 42 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 42 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR H 42 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR H 42 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR H 42 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 42 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 42 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -59 " 0.040 2.00e-02 2.50e+03 2.45e-02 1.51e+01 pdb=" N1 DT I -59 " -0.064 2.00e-02 2.50e+03 pdb=" C2 DT I -59 " 0.015 2.00e-02 2.50e+03 pdb=" O2 DT I -59 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I -59 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I -59 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I -59 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT I -59 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT I -59 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I -59 " -0.001 2.00e-02 2.50e+03 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 4 2.27 - 2.92: 4692 2.92 - 3.58: 19109 3.58 - 4.24: 33457 4.24 - 4.90: 49191 Nonbonded interactions: 106453 Sorted by model distance: nonbonded pdb=" O THR A 80 " pdb=" OD1 ASP A 81 " model vdw 1.607 3.040 nonbonded pdb=" O GLN G 24 " pdb=" CD1 TYR H 40 " model vdw 1.896 3.340 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 48 " model vdw 1.950 3.040 nonbonded pdb=" OG1 THR F 82 " pdb=" OD2 ASP F 85 " model vdw 2.158 3.040 nonbonded pdb=" C THR A 80 " pdb=" OD1 ASP A 81 " model vdw 2.335 3.270 ... (remaining 106448 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' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77)) selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.006 0.069 13172 Z= 0.308 Angle : 0.884 7.104 19130 Z= 0.570 Chirality : 0.052 0.340 2174 Planarity : 0.010 0.135 1340 Dihedral : 28.206 164.979 5706 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.16 % Allowed : 11.94 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 732 helix: 0.81 (0.20), residues: 514 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS C 82 PHE 0.027 0.002 PHE E 84 TYR 0.059 0.004 TYR H 42 ARG 0.010 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.10438 ( 804) hydrogen bonds : angle 3.79437 ( 1987) covalent geometry : bond 0.00577 (13172) covalent geometry : angle 0.88371 (19130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8487 (mmm) cc_final: 0.8263 (mmm) REVERT: C 42 ARG cc_start: 0.8239 (mtp85) cc_final: 0.8034 (mtp85) REVERT: C 68 ASN cc_start: 0.8046 (m-40) cc_final: 0.7754 (m-40) REVERT: C 74 LYS cc_start: 0.7782 (mttt) cc_final: 0.7574 (mttt) REVERT: C 95 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8650 (ttmm) REVERT: C 99 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7569 (mmm160) REVERT: D 57 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8632 (mmmm) REVERT: E 59 GLU cc_start: 0.7810 (pm20) cc_final: 0.7477 (pm20) REVERT: F 25 ASN cc_start: 0.6886 (m-40) cc_final: 0.5997 (m-40) REVERT: G 13 LYS cc_start: 0.8298 (mmmm) cc_final: 0.8036 (mmmm) REVERT: G 18 SER cc_start: 0.8832 (m) cc_final: 0.8608 (p) REVERT: G 63 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8157 (mt) REVERT: G 73 ASN cc_start: 0.8198 (t0) cc_final: 0.7842 (t0) REVERT: H 57 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8410 (mmmm) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.4445 time to fit residues: 128.3129 Evaluate side-chains 207 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 73 ASN D 47 GLN D 84 ASN E 125 GLN F 27 GLN F 75 HIS G 31 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.081930 restraints weight = 21806.279| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.20 r_work: 0.2906 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13172 Z= 0.240 Angle : 0.629 6.126 19130 Z= 0.382 Chirality : 0.039 0.148 2174 Planarity : 0.005 0.041 1340 Dihedral : 30.266 161.239 4238 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.42 % Allowed : 17.58 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.30), residues: 732 helix: 2.91 (0.22), residues: 526 sheet: None (None), residues: 0 loop : 0.04 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.015 0.002 PHE G 25 TYR 0.023 0.002 TYR F 88 ARG 0.009 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 804) hydrogen bonds : angle 2.75195 ( 1987) covalent geometry : bond 0.00536 (13172) covalent geometry : angle 0.62905 (19130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 0.824 Fit side-chains REVERT: A 54 TYR cc_start: 0.8947 (m-80) cc_final: 0.8723 (m-80) REVERT: A 59 GLU cc_start: 0.8085 (pm20) cc_final: 0.7552 (pm20) REVERT: A 60 LEU cc_start: 0.8733 (mp) cc_final: 0.8371 (mt) REVERT: A 116 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8144 (mtm-85) REVERT: C 57 TYR cc_start: 0.8833 (t80) cc_final: 0.8598 (t80) REVERT: C 61 GLU cc_start: 0.7871 (tp30) cc_final: 0.7544 (tp30) REVERT: C 71 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6740 (ttp-110) REVERT: D 52 THR cc_start: 0.8828 (m) cc_final: 0.8465 (p) REVERT: D 91 SER cc_start: 0.8703 (p) cc_final: 0.8450 (p) REVERT: F 79 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8497 (mtmm) REVERT: F 84 MET cc_start: 0.8368 (mmm) cc_final: 0.8126 (mmm) REVERT: G 73 ASN cc_start: 0.8482 (t0) cc_final: 0.8109 (t0) REVERT: H 83 TYR cc_start: 0.8137 (m-10) cc_final: 0.7876 (m-10) REVERT: H 116 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8783 (ttpp) outliers start: 15 outliers final: 9 residues processed: 241 average time/residue: 0.3667 time to fit residues: 112.2919 Evaluate side-chains 231 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 47 GLN D 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.082068 restraints weight = 21748.994| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.29 r_work: 0.2881 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13172 Z= 0.190 Angle : 0.573 8.367 19130 Z= 0.349 Chirality : 0.035 0.147 2174 Planarity : 0.004 0.042 1340 Dihedral : 29.966 163.010 4236 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.39 % Allowed : 22.10 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.30), residues: 732 helix: 3.35 (0.22), residues: 526 sheet: None (None), residues: 0 loop : 0.09 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.016 0.001 PHE F 100 TYR 0.031 0.002 TYR D 83 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 804) hydrogen bonds : angle 2.54671 ( 1987) covalent geometry : bond 0.00416 (13172) covalent geometry : angle 0.57344 (19130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8103 (pm20) cc_final: 0.7579 (pm20) REVERT: C 40 SER cc_start: 0.8720 (m) cc_final: 0.8505 (p) REVERT: C 57 TYR cc_start: 0.8840 (t80) cc_final: 0.8573 (t80) REVERT: D 42 TYR cc_start: 0.8181 (t80) cc_final: 0.7962 (t80) REVERT: D 91 SER cc_start: 0.8701 (p) cc_final: 0.8461 (p) REVERT: G 73 ASN cc_start: 0.8452 (t0) cc_final: 0.8133 (t0) REVERT: H 83 TYR cc_start: 0.8162 (m-10) cc_final: 0.7878 (m-10) outliers start: 21 outliers final: 15 residues processed: 232 average time/residue: 0.3731 time to fit residues: 109.7996 Evaluate side-chains 234 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 47 GLN D 82 HIS F 27 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.082745 restraints weight = 21469.416| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.28 r_work: 0.2902 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13172 Z= 0.179 Angle : 0.559 9.510 19130 Z= 0.340 Chirality : 0.034 0.144 2174 Planarity : 0.004 0.041 1340 Dihedral : 29.932 163.283 4236 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.39 % Allowed : 23.06 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.30), residues: 732 helix: 3.33 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.08 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 82 PHE 0.013 0.001 PHE F 100 TYR 0.041 0.002 TYR D 83 ARG 0.010 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 804) hydrogen bonds : angle 2.46868 ( 1987) covalent geometry : bond 0.00391 (13172) covalent geometry : angle 0.55947 (19130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 0.804 Fit side-chains REVERT: A 59 GLU cc_start: 0.8039 (pm20) cc_final: 0.7510 (pm20) REVERT: B 25 ASN cc_start: 0.7286 (m-40) cc_final: 0.7062 (m-40) REVERT: B 88 TYR cc_start: 0.8674 (m-10) cc_final: 0.7979 (m-10) REVERT: C 35 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8330 (ttp80) REVERT: C 40 SER cc_start: 0.8751 (m) cc_final: 0.8528 (p) REVERT: C 57 TYR cc_start: 0.8865 (t80) cc_final: 0.8582 (t80) REVERT: D 42 TYR cc_start: 0.8227 (t80) cc_final: 0.8002 (t80) REVERT: D 46 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8840 (mmtp) REVERT: D 83 TYR cc_start: 0.8088 (m-10) cc_final: 0.7780 (m-80) REVERT: D 91 SER cc_start: 0.8690 (p) cc_final: 0.8465 (p) REVERT: E 59 GLU cc_start: 0.7990 (pm20) cc_final: 0.7391 (pm20) REVERT: E 73 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8103 (tm-30) REVERT: G 39 TYR cc_start: 0.8583 (m-80) cc_final: 0.8295 (m-10) REVERT: G 73 ASN cc_start: 0.8494 (t0) cc_final: 0.8158 (t0) REVERT: H 83 TYR cc_start: 0.8077 (m-10) cc_final: 0.7876 (m-10) outliers start: 21 outliers final: 15 residues processed: 242 average time/residue: 0.3772 time to fit residues: 116.7103 Evaluate side-chains 242 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 47 GLN D 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.079086 restraints weight = 21626.006| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.29 r_work: 0.2834 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13172 Z= 0.252 Angle : 0.604 9.708 19130 Z= 0.364 Chirality : 0.038 0.156 2174 Planarity : 0.005 0.044 1340 Dihedral : 30.033 164.278 4236 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 6.29 % Allowed : 21.13 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.30), residues: 732 helix: 3.14 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.34 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 49 PHE 0.017 0.002 PHE F 100 TYR 0.035 0.002 TYR D 83 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 804) hydrogen bonds : angle 2.63173 ( 1987) covalent geometry : bond 0.00561 (13172) covalent geometry : angle 0.60405 (19130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8058 (pm20) cc_final: 0.7537 (pm20) REVERT: A 60 LEU cc_start: 0.8801 (mp) cc_final: 0.8490 (mt) REVERT: B 25 ASN cc_start: 0.7421 (m-40) cc_final: 0.7177 (m-40) REVERT: B 73 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8615 (t) REVERT: B 88 TYR cc_start: 0.8821 (m-10) cc_final: 0.8458 (m-10) REVERT: D 42 TYR cc_start: 0.8226 (t80) cc_final: 0.8017 (t80) REVERT: D 79 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8368 (ttm-80) REVERT: E 59 GLU cc_start: 0.8115 (pm20) cc_final: 0.7796 (pm20) REVERT: E 73 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8092 (tm-30) REVERT: G 73 ASN cc_start: 0.8497 (t0) cc_final: 0.8143 (t0) REVERT: H 83 TYR cc_start: 0.8089 (m-10) cc_final: 0.7785 (m-10) REVERT: H 87 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.7898 (p) REVERT: H 113 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7993 (mm-30) outliers start: 39 outliers final: 29 residues processed: 239 average time/residue: 0.3594 time to fit residues: 108.6651 Evaluate side-chains 255 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 73 ASN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.094182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.078824 restraints weight = 22063.640| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.29 r_work: 0.2824 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13172 Z= 0.253 Angle : 0.605 11.646 19130 Z= 0.363 Chirality : 0.038 0.165 2174 Planarity : 0.005 0.045 1340 Dihedral : 30.060 165.958 4236 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.48 % Allowed : 23.55 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.30), residues: 732 helix: 3.04 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.36 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.016 0.002 PHE F 100 TYR 0.029 0.002 TYR D 83 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 804) hydrogen bonds : angle 2.59088 ( 1987) covalent geometry : bond 0.00563 (13172) covalent geometry : angle 0.60471 (19130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.829 Fit side-chains REVERT: A 59 GLU cc_start: 0.8094 (pm20) cc_final: 0.7528 (pm20) REVERT: A 60 LEU cc_start: 0.8804 (mp) cc_final: 0.8490 (mt) REVERT: B 25 ASN cc_start: 0.7407 (m-40) cc_final: 0.7141 (m-40) REVERT: B 88 TYR cc_start: 0.8857 (m-10) cc_final: 0.7834 (m-10) REVERT: C 64 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: D 42 TYR cc_start: 0.8179 (t80) cc_final: 0.7946 (t80) REVERT: D 83 TYR cc_start: 0.8205 (m-10) cc_final: 0.7681 (m-80) REVERT: E 59 GLU cc_start: 0.8220 (pm20) cc_final: 0.7861 (pm20) REVERT: E 73 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8112 (tm-30) REVERT: F 77 LYS cc_start: 0.9010 (mtmm) cc_final: 0.8792 (mtmm) REVERT: G 73 ASN cc_start: 0.8542 (t0) cc_final: 0.8185 (t0) REVERT: H 83 TYR cc_start: 0.8079 (m-10) cc_final: 0.7724 (m-10) REVERT: H 87 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8047 (p) REVERT: H 113 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7970 (mm-30) outliers start: 34 outliers final: 27 residues processed: 239 average time/residue: 0.3823 time to fit residues: 115.4979 Evaluate side-chains 254 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 73 ASN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.094214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078850 restraints weight = 21865.147| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.27 r_work: 0.2831 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13172 Z= 0.243 Angle : 0.600 12.374 19130 Z= 0.360 Chirality : 0.037 0.169 2174 Planarity : 0.005 0.045 1340 Dihedral : 30.110 167.230 4236 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 6.29 % Allowed : 23.06 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.30), residues: 732 helix: 3.03 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 49 PHE 0.013 0.002 PHE F 100 TYR 0.024 0.002 TYR D 83 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 804) hydrogen bonds : angle 2.56261 ( 1987) covalent geometry : bond 0.00540 (13172) covalent geometry : angle 0.59990 (19130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.899 Fit side-chains REVERT: A 59 GLU cc_start: 0.8110 (pm20) cc_final: 0.7551 (pm20) REVERT: B 25 ASN cc_start: 0.7404 (m-40) cc_final: 0.7196 (m-40) REVERT: B 73 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8561 (t) REVERT: C 64 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: D 42 TYR cc_start: 0.8031 (t80) cc_final: 0.7739 (t80) REVERT: D 48 VAL cc_start: 0.8987 (t) cc_final: 0.8784 (p) REVERT: D 51 ASP cc_start: 0.8469 (p0) cc_final: 0.8014 (p0) REVERT: D 52 THR cc_start: 0.9010 (t) cc_final: 0.8677 (p) REVERT: D 83 TYR cc_start: 0.8216 (m-10) cc_final: 0.7905 (m-80) REVERT: E 59 GLU cc_start: 0.8202 (pm20) cc_final: 0.7874 (pm20) REVERT: E 73 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 77 LYS cc_start: 0.9019 (mtmm) cc_final: 0.8798 (mtmm) REVERT: G 73 ASN cc_start: 0.8556 (t0) cc_final: 0.8232 (t0) REVERT: H 83 TYR cc_start: 0.8051 (m-10) cc_final: 0.7603 (m-10) REVERT: H 87 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8022 (p) outliers start: 39 outliers final: 34 residues processed: 241 average time/residue: 0.3675 time to fit residues: 112.1324 Evaluate side-chains 261 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 73 ASN D 82 HIS F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083079 restraints weight = 21589.005| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.27 r_work: 0.2907 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13172 Z= 0.161 Angle : 0.560 12.133 19130 Z= 0.336 Chirality : 0.033 0.165 2174 Planarity : 0.004 0.045 1340 Dihedral : 29.938 168.436 4236 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.23 % Allowed : 26.94 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.31), residues: 732 helix: 3.31 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 82 PHE 0.010 0.001 PHE F 100 TYR 0.023 0.001 TYR D 83 ARG 0.012 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 804) hydrogen bonds : angle 2.40661 ( 1987) covalent geometry : bond 0.00346 (13172) covalent geometry : angle 0.55995 (19130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.816 Fit side-chains REVERT: A 59 GLU cc_start: 0.8068 (pm20) cc_final: 0.7523 (pm20) REVERT: D 51 ASP cc_start: 0.8445 (p0) cc_final: 0.7989 (p0) REVERT: D 52 THR cc_start: 0.8985 (t) cc_final: 0.8720 (p) REVERT: D 83 TYR cc_start: 0.8117 (m-10) cc_final: 0.7819 (m-80) REVERT: E 59 GLU cc_start: 0.8136 (pm20) cc_final: 0.7770 (pm20) REVERT: E 73 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8094 (tm-30) REVERT: G 73 ASN cc_start: 0.8530 (t0) cc_final: 0.8217 (t0) REVERT: H 48 VAL cc_start: 0.9018 (t) cc_final: 0.8793 (p) REVERT: H 83 TYR cc_start: 0.8011 (m-10) cc_final: 0.7776 (m-10) REVERT: H 87 SER cc_start: 0.8330 (m) cc_final: 0.7994 (p) outliers start: 20 outliers final: 16 residues processed: 231 average time/residue: 0.3732 time to fit residues: 108.9615 Evaluate side-chains 237 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082902 restraints weight = 21462.809| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.26 r_work: 0.2904 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13172 Z= 0.172 Angle : 0.570 12.865 19130 Z= 0.339 Chirality : 0.034 0.168 2174 Planarity : 0.004 0.047 1340 Dihedral : 29.948 170.091 4236 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.55 % Allowed : 27.10 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.31), residues: 732 helix: 3.26 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 49 PHE 0.013 0.001 PHE F 100 TYR 0.020 0.002 TYR D 83 ARG 0.011 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 804) hydrogen bonds : angle 2.45957 ( 1987) covalent geometry : bond 0.00373 (13172) covalent geometry : angle 0.56951 (19130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.937 Fit side-chains REVERT: A 59 GLU cc_start: 0.8088 (pm20) cc_final: 0.7534 (pm20) REVERT: B 74 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8199 (mm-30) REVERT: C 64 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7908 (tp30) REVERT: D 46 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8812 (mmtm) REVERT: D 51 ASP cc_start: 0.8444 (p0) cc_final: 0.7944 (p0) REVERT: D 52 THR cc_start: 0.8986 (t) cc_final: 0.8737 (p) REVERT: D 83 TYR cc_start: 0.8098 (m-10) cc_final: 0.7768 (m-80) REVERT: E 59 GLU cc_start: 0.8134 (pm20) cc_final: 0.7768 (pm20) REVERT: E 73 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8087 (tm-30) REVERT: G 73 ASN cc_start: 0.8519 (t0) cc_final: 0.8210 (t0) REVERT: H 83 TYR cc_start: 0.7993 (m-10) cc_final: 0.7662 (m-10) REVERT: H 87 SER cc_start: 0.8359 (m) cc_final: 0.8031 (p) REVERT: H 113 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7907 (mm-30) outliers start: 22 outliers final: 19 residues processed: 237 average time/residue: 0.3596 time to fit residues: 108.1732 Evaluate side-chains 242 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 125 GLN C 73 ASN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.083135 restraints weight = 21470.486| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.26 r_work: 0.2904 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13172 Z= 0.177 Angle : 0.566 12.590 19130 Z= 0.339 Chirality : 0.034 0.167 2174 Planarity : 0.004 0.048 1340 Dihedral : 29.929 171.705 4236 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.55 % Allowed : 26.61 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.31), residues: 732 helix: 3.25 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 49 PHE 0.016 0.001 PHE F 100 TYR 0.018 0.002 TYR D 83 ARG 0.011 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 804) hydrogen bonds : angle 2.44849 ( 1987) covalent geometry : bond 0.00384 (13172) covalent geometry : angle 0.56640 (19130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.907 Fit side-chains REVERT: A 59 GLU cc_start: 0.8078 (pm20) cc_final: 0.7522 (pm20) REVERT: B 74 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8171 (mm-30) REVERT: C 64 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: D 48 VAL cc_start: 0.8933 (p) cc_final: 0.8714 (p) REVERT: D 51 ASP cc_start: 0.8472 (p0) cc_final: 0.8020 (p0) REVERT: D 52 THR cc_start: 0.8989 (t) cc_final: 0.8635 (p) REVERT: D 83 TYR cc_start: 0.8079 (m-10) cc_final: 0.7787 (m-80) REVERT: E 59 GLU cc_start: 0.8165 (pm20) cc_final: 0.7804 (pm20) REVERT: E 73 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8093 (tm-30) REVERT: G 73 ASN cc_start: 0.8531 (t0) cc_final: 0.8226 (t0) REVERT: H 83 TYR cc_start: 0.8012 (m-10) cc_final: 0.7672 (m-10) REVERT: H 87 SER cc_start: 0.8398 (m) cc_final: 0.8086 (p) REVERT: H 113 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7929 (mm-30) outliers start: 22 outliers final: 19 residues processed: 235 average time/residue: 0.3674 time to fit residues: 108.9123 Evaluate side-chains 241 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 93 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 125 GLN C 73 ASN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083078 restraints weight = 21629.997| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.28 r_work: 0.2904 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13172 Z= 0.181 Angle : 0.571 12.282 19130 Z= 0.341 Chirality : 0.034 0.169 2174 Planarity : 0.005 0.047 1340 Dihedral : 29.945 174.498 4236 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.55 % Allowed : 26.45 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.31), residues: 732 helix: 3.19 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.017 0.001 PHE F 100 TYR 0.022 0.002 TYR D 83 ARG 0.011 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 804) hydrogen bonds : angle 2.49628 ( 1987) covalent geometry : bond 0.00393 (13172) covalent geometry : angle 0.57122 (19130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5685.20 seconds wall clock time: 98 minutes 41.84 seconds (5921.84 seconds total)