Starting phenix.real_space_refine on Wed Jul 30 04:59:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jla_36390/07_2025/8jla_36390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jla_36390/07_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_36390/07_2025/8jla_36390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jla_36390/07_2025/8jla_36390.map" model { file = "/net/cci-nas-00/data/ceres_data/8jla_36390/07_2025/8jla_36390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jla_36390/07_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-5711/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: 7.92, per 1000 atoms: 0.64 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: 2.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 6.59 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: 5.01 Time building geometry restraints manager: 3.44 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: 1.370 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: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.230 Set scattering table: 0.180 Process input model: 35.420 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- 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 : 0.975 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: 0.4595 time to fit residues: 133.0231 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 : 0.928 ------------------------------------------------------------------------------- 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 = 0.081931 restraints weight = 21805.297| |-----------------------------------------------------------------------------| 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 2.75194 ( 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 : 0.837 Fit side-chains REVERT: A 54 TYR cc_start: 0.8946 (m-80) cc_final: 0.8723 (m-80) REVERT: A 59 GLU cc_start: 0.8083 (pm20) cc_final: 0.7548 (pm20) REVERT: A 60 LEU cc_start: 0.8731 (mp) cc_final: 0.8368 (mt) REVERT: A 116 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8141 (mtm-85) REVERT: C 57 TYR cc_start: 0.8834 (t80) cc_final: 0.8599 (t80) REVERT: C 61 GLU cc_start: 0.7868 (tp30) cc_final: 0.7540 (tp30) REVERT: C 71 ARG cc_start: 0.7119 (ttp-110) cc_final: 0.6738 (ttp-110) REVERT: D 52 THR cc_start: 0.8830 (m) cc_final: 0.8467 (p) REVERT: D 91 SER cc_start: 0.8704 (p) cc_final: 0.8450 (p) REVERT: F 79 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8496 (mtmm) REVERT: F 84 MET cc_start: 0.8370 (mmm) cc_final: 0.8128 (mmm) REVERT: G 73 ASN cc_start: 0.8480 (t0) cc_final: 0.8108 (t0) REVERT: H 83 TYR cc_start: 0.8132 (m-10) cc_final: 0.7874 (m-10) REVERT: H 116 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8785 (ttpp) outliers start: 15 outliers final: 9 residues processed: 241 average time/residue: 0.3687 time to fit residues: 112.8758 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 : 0.847 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3241 r_free = 0.3241 target = 0.094898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079503 restraints weight = 21822.132| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.31 r_work: 0.2845 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13172 Z= 0.234 Angle : 0.602 8.196 19130 Z= 0.365 Chirality : 0.038 0.146 2174 Planarity : 0.005 0.043 1340 Dihedral : 30.055 163.235 4236 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.35 % Allowed : 21.45 % Favored : 74.19 % 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: 3.54 (0.30), residues: 732 helix: 3.20 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.018 0.002 PHE F 100 TYR 0.034 0.002 TYR D 83 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 804) hydrogen bonds : angle 2.63648 ( 1987) covalent geometry : bond 0.00521 (13172) covalent geometry : angle 0.60230 (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 259 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8106 (pm20) cc_final: 0.7600 (pm20) REVERT: B 25 ASN cc_start: 0.7314 (m-40) cc_final: 0.7101 (m-40) REVERT: B 88 TYR cc_start: 0.8838 (m-80) cc_final: 0.7545 (m-10) REVERT: C 40 SER cc_start: 0.8827 (m) cc_final: 0.8620 (p) REVERT: C 57 TYR cc_start: 0.8834 (t80) cc_final: 0.8577 (t80) REVERT: D 42 TYR cc_start: 0.8207 (t80) cc_final: 0.7994 (t80) REVERT: D 52 THR cc_start: 0.8890 (m) cc_final: 0.8689 (t) REVERT: D 83 TYR cc_start: 0.8179 (m-10) cc_final: 0.7312 (m-80) REVERT: D 91 SER cc_start: 0.8730 (p) cc_final: 0.8493 (p) REVERT: F 84 MET cc_start: 0.8472 (mmm) cc_final: 0.8167 (mmm) REVERT: G 73 ASN cc_start: 0.8439 (t0) cc_final: 0.8104 (t0) REVERT: H 83 TYR cc_start: 0.8208 (m-10) cc_final: 0.7884 (m-10) outliers start: 27 outliers final: 19 residues processed: 241 average time/residue: 0.3768 time to fit residues: 115.1668 Evaluate side-chains 244 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL 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 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 87 SER Chi-restraints excluded: chain H residue 118 VAL 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: 2.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 47 GLN D 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.082185 restraints weight = 21520.517| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.28 r_work: 0.2891 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13172 Z= 0.178 Angle : 0.557 9.435 19130 Z= 0.341 Chirality : 0.034 0.145 2174 Planarity : 0.004 0.042 1340 Dihedral : 29.938 163.556 4236 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.03 % Allowed : 23.87 % Favored : 72.10 % 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: 3.65 (0.30), residues: 732 helix: 3.31 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 82 PHE 0.014 0.001 PHE F 100 TYR 0.020 0.001 TYR D 83 ARG 0.010 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 804) hydrogen bonds : angle 2.46015 ( 1987) covalent geometry : bond 0.00391 (13172) covalent geometry : angle 0.55727 (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: 25 poor density : 229 time to evaluate : 0.995 Fit side-chains REVERT: A 59 GLU cc_start: 0.8046 (pm20) cc_final: 0.7520 (pm20) REVERT: B 25 ASN cc_start: 0.7320 (m-40) cc_final: 0.7092 (m-40) REVERT: C 57 TYR cc_start: 0.8821 (t80) cc_final: 0.8534 (t80) REVERT: D 42 TYR cc_start: 0.8234 (t80) cc_final: 0.8009 (t80) REVERT: D 83 TYR cc_start: 0.8156 (m-10) cc_final: 0.7825 (m-80) REVERT: D 91 SER cc_start: 0.8696 (p) cc_final: 0.8474 (p) REVERT: F 84 MET cc_start: 0.8399 (mmm) cc_final: 0.8092 (mmm) REVERT: G 73 ASN cc_start: 0.8511 (t0) cc_final: 0.8170 (t0) REVERT: H 83 TYR cc_start: 0.8144 (m-10) cc_final: 0.7918 (m-10) REVERT: H 87 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7854 (p) outliers start: 25 outliers final: 18 residues processed: 239 average time/residue: 0.3887 time to fit residues: 118.3612 Evaluate side-chains 244 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 B residue 96 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 85 LYS 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 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 78 SER Chi-restraints excluded: chain H residue 87 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: 3.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.077273 restraints weight = 21757.214| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.28 r_work: 0.2800 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 13172 Z= 0.304 Angle : 0.639 11.109 19130 Z= 0.384 Chirality : 0.041 0.163 2174 Planarity : 0.005 0.049 1340 Dihedral : 30.155 165.319 4236 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.29 % Allowed : 21.77 % Favored : 71.94 % 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: 3.13 (0.30), residues: 732 helix: 2.97 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 49 PHE 0.017 0.002 PHE F 100 TYR 0.019 0.002 TYR D 83 ARG 0.010 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 804) hydrogen bonds : angle 2.71328 ( 1987) covalent geometry : bond 0.00683 (13172) covalent geometry : angle 0.63949 (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 269 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.871 Fit side-chains REVERT: A 59 GLU cc_start: 0.8109 (pm20) cc_final: 0.7590 (pm20) REVERT: A 60 LEU cc_start: 0.8783 (mp) cc_final: 0.8483 (mt) REVERT: B 25 ASN cc_start: 0.7395 (m-40) cc_final: 0.7152 (m-40) REVERT: B 88 TYR cc_start: 0.8951 (m-10) cc_final: 0.7776 (m-10) REVERT: D 42 TYR cc_start: 0.8142 (t80) cc_final: 0.7886 (t80) REVERT: D 51 ASP cc_start: 0.8482 (p0) cc_final: 0.8074 (p0) REVERT: D 83 TYR cc_start: 0.8279 (m-10) cc_final: 0.7632 (m-10) REVERT: D 91 SER cc_start: 0.8794 (p) cc_final: 0.8573 (p) REVERT: E 73 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8091 (tm-30) REVERT: G 73 ASN cc_start: 0.8542 (t0) cc_final: 0.8170 (t0) REVERT: H 35 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7919 (mt-10) REVERT: H 83 TYR cc_start: 0.8186 (m-10) cc_final: 0.7605 (m-10) REVERT: H 113 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8019 (mm-30) outliers start: 39 outliers final: 28 residues processed: 239 average time/residue: 0.3798 time to fit residues: 115.0202 Evaluate side-chains 254 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 59 LYS 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 107 VAL Chi-restraints excluded: chain C residue 110 ASN 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 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 G residue 19 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 36 SER 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 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081244 restraints weight = 21854.620| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.28 r_work: 0.2875 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3831 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= 0.181 Angle : 0.565 11.324 19130 Z= 0.343 Chirality : 0.034 0.158 2174 Planarity : 0.004 0.046 1340 Dihedral : 29.962 165.546 4236 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.03 % Allowed : 24.52 % Favored : 71.45 % 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: 3.39 (0.31), residues: 732 helix: 3.18 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 82 PHE 0.011 0.001 PHE F 100 TYR 0.013 0.001 TYR C 57 ARG 0.010 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 804) hydrogen bonds : angle 2.49142 ( 1987) covalent geometry : bond 0.00394 (13172) covalent geometry : angle 0.56549 (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 253 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.839 Fit side-chains REVERT: A 59 GLU cc_start: 0.8085 (pm20) cc_final: 0.7537 (pm20) REVERT: C 57 TYR cc_start: 0.8931 (t80) cc_final: 0.8390 (t80) REVERT: C 64 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7916 (tp30) REVERT: D 42 TYR cc_start: 0.8148 (t80) cc_final: 0.7900 (t80) REVERT: D 51 ASP cc_start: 0.8495 (p0) cc_final: 0.8110 (p0) REVERT: D 83 TYR cc_start: 0.8192 (m-10) cc_final: 0.7858 (m-10) REVERT: D 91 SER cc_start: 0.8703 (p) cc_final: 0.8452 (p) REVERT: E 73 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8133 (tm-30) REVERT: G 19 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8651 (p) REVERT: G 73 ASN cc_start: 0.8537 (t0) cc_final: 0.8218 (t0) REVERT: H 35 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7917 (mt-10) REVERT: H 83 TYR cc_start: 0.8082 (m-10) cc_final: 0.7852 (m-10) outliers start: 25 outliers final: 20 residues processed: 236 average time/residue: 0.3796 time to fit residues: 113.5995 Evaluate side-chains 244 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 80 THR 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 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 E residue 87 SER Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 55 SER 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: 0.7980 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.080047 restraints weight = 21739.297| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.27 r_work: 0.2849 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13172 Z= 0.218 Angle : 0.591 11.755 19130 Z= 0.355 Chirality : 0.036 0.170 2174 Planarity : 0.005 0.046 1340 Dihedral : 30.032 167.107 4236 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.52 % Allowed : 25.32 % Favored : 70.16 % 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: 3.33 (0.30), residues: 732 helix: 3.12 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.010 0.001 PHE F 100 TYR 0.018 0.002 TYR G 39 ARG 0.011 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 804) hydrogen bonds : angle 2.55799 ( 1987) covalent geometry : bond 0.00485 (13172) covalent geometry : angle 0.59055 (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 255 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.903 Fit side-chains REVERT: A 59 GLU cc_start: 0.8094 (pm20) cc_final: 0.7525 (pm20) REVERT: C 64 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: D 42 TYR cc_start: 0.8106 (t80) cc_final: 0.7879 (t80) REVERT: D 51 ASP cc_start: 0.8494 (p0) cc_final: 0.8062 (p0) REVERT: D 83 TYR cc_start: 0.8242 (m-10) cc_final: 0.7873 (m-10) REVERT: D 91 SER cc_start: 0.8772 (p) cc_final: 0.8524 (p) REVERT: E 73 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8132 (tm-30) REVERT: F 77 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8778 (mtmm) REVERT: G 73 ASN cc_start: 0.8544 (t0) cc_final: 0.8213 (t0) REVERT: H 35 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7903 (mt-10) REVERT: H 83 TYR cc_start: 0.8043 (m-10) cc_final: 0.7776 (m-10) REVERT: H 87 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7939 (p) REVERT: H 113 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7959 (mm-30) outliers start: 28 outliers final: 21 residues processed: 236 average time/residue: 0.3850 time to fit residues: 114.9358 Evaluate side-chains 248 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 80 THR 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 B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 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 87 SER 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: 4.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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 D 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080908 restraints weight = 21649.451| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.27 r_work: 0.2870 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4016 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= 0.192 Angle : 0.584 12.474 19130 Z= 0.349 Chirality : 0.035 0.195 2174 Planarity : 0.005 0.077 1340 Dihedral : 30.006 167.616 4236 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.71 % Allowed : 25.97 % Favored : 70.32 % 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: 3.40 (0.31), residues: 732 helix: 3.17 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 49 PHE 0.011 0.001 PHE E 78 TYR 0.012 0.001 TYR G 57 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 804) hydrogen bonds : angle 2.52618 ( 1987) covalent geometry : bond 0.00423 (13172) covalent geometry : angle 0.58429 (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 247 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.901 Fit side-chains REVERT: A 59 GLU cc_start: 0.8092 (pm20) cc_final: 0.7517 (pm20) REVERT: C 57 TYR cc_start: 0.8934 (t80) cc_final: 0.8344 (t80) REVERT: C 64 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: D 42 TYR cc_start: 0.8009 (t80) cc_final: 0.7763 (t80) REVERT: D 51 ASP cc_start: 0.8454 (p0) cc_final: 0.8012 (p0) REVERT: D 83 TYR cc_start: 0.8207 (m-10) cc_final: 0.7871 (m-10) REVERT: D 91 SER cc_start: 0.8718 (p) cc_final: 0.8469 (p) REVERT: E 73 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8141 (tm-30) REVERT: F 77 LYS cc_start: 0.9013 (mtmm) cc_final: 0.8796 (mtmm) REVERT: G 73 ASN cc_start: 0.8549 (t0) cc_final: 0.8223 (t0) REVERT: H 83 TYR cc_start: 0.7994 (m-10) cc_final: 0.7699 (m-10) REVERT: H 87 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7870 (p) REVERT: H 113 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7958 (mm-30) outliers start: 23 outliers final: 17 residues processed: 231 average time/residue: 0.3800 time to fit residues: 111.3205 Evaluate side-chains 242 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 A residue 117 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 109 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 48 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 D 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.080985 restraints weight = 21481.836| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.26 r_work: 0.2870 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4109 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= 0.201 Angle : 0.583 11.803 19130 Z= 0.350 Chirality : 0.035 0.170 2174 Planarity : 0.004 0.046 1340 Dihedral : 30.033 169.329 4236 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.03 % Allowed : 26.45 % Favored : 69.52 % 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: 3.38 (0.31), residues: 732 helix: 3.14 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 49 PHE 0.012 0.001 PHE F 100 TYR 0.012 0.001 TYR G 57 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 804) hydrogen bonds : angle 2.53315 ( 1987) covalent geometry : bond 0.00444 (13172) covalent geometry : angle 0.58279 (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: 25 poor density : 223 time to evaluate : 0.835 Fit side-chains REVERT: A 59 GLU cc_start: 0.8102 (pm20) cc_final: 0.7568 (pm20) REVERT: C 64 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7908 (tp30) REVERT: D 34 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8227 (mmmm) REVERT: D 51 ASP cc_start: 0.8448 (p0) cc_final: 0.7994 (p0) REVERT: D 52 THR cc_start: 0.8964 (t) cc_final: 0.8665 (p) REVERT: D 83 TYR cc_start: 0.8206 (m-10) cc_final: 0.7887 (m-10) REVERT: D 91 SER cc_start: 0.8760 (p) cc_final: 0.8505 (p) REVERT: E 73 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8115 (tm-30) REVERT: F 77 LYS cc_start: 0.9015 (mtmm) cc_final: 0.8800 (mtmm) REVERT: G 73 ASN cc_start: 0.8555 (t0) cc_final: 0.8228 (t0) REVERT: H 83 TYR cc_start: 0.7992 (m-10) cc_final: 0.7698 (m-10) REVERT: H 87 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.7990 (p) outliers start: 25 outliers final: 21 residues processed: 231 average time/residue: 0.3902 time to fit residues: 114.0057 Evaluate side-chains 244 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 80 THR 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 B residue 92 ARG 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 D residue 85 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 109 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 48 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 D 82 HIS F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.080870 restraints weight = 21512.980| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.26 r_work: 0.2867 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.005 0.040 13172 Z= 0.205 Angle : 0.597 13.441 19130 Z= 0.354 Chirality : 0.035 0.172 2174 Planarity : 0.005 0.048 1340 Dihedral : 30.030 170.973 4236 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.03 % Allowed : 26.29 % Favored : 69.68 % 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 (0.31), residues: 732 helix: 3.13 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 49 PHE 0.013 0.001 PHE F 100 TYR 0.012 0.001 TYR G 57 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 804) hydrogen bonds : angle 2.56630 ( 1987) covalent geometry : bond 0.00453 (13172) covalent geometry : angle 0.59728 (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 248 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 1.037 Fit side-chains REVERT: A 59 GLU cc_start: 0.8107 (pm20) cc_final: 0.7570 (pm20) REVERT: C 64 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: D 34 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8230 (mmmm) REVERT: D 51 ASP cc_start: 0.8464 (p0) cc_final: 0.8004 (p0) REVERT: D 52 THR cc_start: 0.9024 (t) cc_final: 0.8787 (p) REVERT: D 83 TYR cc_start: 0.8196 (m-10) cc_final: 0.7882 (m-10) REVERT: D 91 SER cc_start: 0.8719 (p) cc_final: 0.8463 (p) REVERT: E 73 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8131 (tm-30) REVERT: F 77 LYS cc_start: 0.9007 (mtmm) cc_final: 0.8801 (mtmm) REVERT: G 73 ASN cc_start: 0.8554 (t0) cc_final: 0.8227 (t0) REVERT: H 83 TYR cc_start: 0.7987 (m-10) cc_final: 0.7688 (m-10) REVERT: H 87 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8017 (p) REVERT: H 113 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7955 (mm-30) outliers start: 25 outliers final: 21 residues processed: 231 average time/residue: 0.4835 time to fit residues: 141.3787 Evaluate side-chains 246 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 80 THR 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 64 GLU Chi-restraints excluded: chain C residue 71 ARG 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 E residue 109 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 48 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 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: 0.7980 chunk 25 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 D 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082408 restraints weight = 21557.153| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.26 r_work: 0.2895 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13172 Z= 0.167 Angle : 0.585 13.152 19130 Z= 0.346 Chirality : 0.034 0.169 2174 Planarity : 0.005 0.052 1340 Dihedral : 29.982 171.951 4236 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.06 % Allowed : 27.90 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.31), residues: 732 helix: 3.25 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 82 PHE 0.011 0.001 PHE F 100 TYR 0.014 0.001 TYR D 121 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 804) hydrogen bonds : angle 2.51912 ( 1987) covalent geometry : bond 0.00361 (13172) covalent geometry : angle 0.58450 (19130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6418.68 seconds wall clock time: 112 minutes 35.51 seconds (6755.51 seconds total)