Starting phenix.real_space_refine on Fri Feb 14 23:42:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5k_10700/02_2025/6y5k_10700.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5k_10700/02_2025/6y5k_10700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5k_10700/02_2025/6y5k_10700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5k_10700/02_2025/6y5k_10700.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5k_10700/02_2025/6y5k_10700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5k_10700/02_2025/6y5k_10700.cif" } resolution = 4.2 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= 0.062 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6609 2.51 5 N 1854 2.21 5 O 2097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10614 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 292} Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1096 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: D, F, C, E Time building chain proxies: 6.51, per 1000 atoms: 0.61 Number of scatterers: 10614 At special positions: 0 Unit cell: (101.091, 98.917, 159.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2097 8.00 N 1854 7.00 C 6609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=1.75 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.46 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.00 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG C 401 " - " ASN C 38 " " NAG E 401 " - " ASN E 38 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 36 sheets defined 32.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.117A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.699A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 126 Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.116A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.699A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.116A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.700A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 126 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 Processing helix chain 'F' and resid 38 through 126 Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.964A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.703A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.965A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.703A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.495A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 removed outlier: 5.964A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.702A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD7, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AD9, first strand: chain 'F' and resid 130 through 132 483 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3567 1.34 - 1.46: 2442 1.46 - 1.59: 4743 1.59 - 1.71: 0 1.71 - 1.83: 72 Bond restraints: 10824 Sorted by residual: bond pdb=" N CYS A 305 " pdb=" CA CYS A 305 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.17e-02 7.31e+03 9.71e+00 bond pdb=" N CYS C 305 " pdb=" CA CYS C 305 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.17e-02 7.31e+03 9.44e+00 bond pdb=" N CYS E 305 " pdb=" CA CYS E 305 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.17e-02 7.31e+03 9.32e+00 bond pdb=" N LYS C 50 " pdb=" CA LYS C 50 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.22e+00 bond pdb=" N LYS E 50 " pdb=" CA LYS E 50 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.23e-02 6.61e+03 7.15e+00 ... (remaining 10819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 14282 2.06 - 4.12: 359 4.12 - 6.17: 35 6.17 - 8.23: 3 8.23 - 10.29: 6 Bond angle restraints: 14685 Sorted by residual: angle pdb=" C CYS C 305 " pdb=" CA CYS C 305 " pdb=" CB CYS C 305 " ideal model delta sigma weight residual 110.47 104.21 6.26 1.77e+00 3.19e-01 1.25e+01 angle pdb=" C CYS A 305 " pdb=" CA CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sigma weight residual 110.47 104.21 6.26 1.77e+00 3.19e-01 1.25e+01 angle pdb=" C CYS E 305 " pdb=" CA CYS E 305 " pdb=" CB CYS E 305 " ideal model delta sigma weight residual 110.47 104.22 6.25 1.77e+00 3.19e-01 1.25e+01 angle pdb=" O CYS C 76 " pdb=" C CYS C 76 " pdb=" N ASP C 77 " ideal model delta sigma weight residual 121.99 125.98 -3.99 1.24e+00 6.50e-01 1.03e+01 angle pdb=" O CYS E 76 " pdb=" C CYS E 76 " pdb=" N ASP E 77 " ideal model delta sigma weight residual 121.99 125.97 -3.98 1.24e+00 6.50e-01 1.03e+01 ... (remaining 14680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6016 17.15 - 34.31: 440 34.31 - 51.46: 139 51.46 - 68.61: 13 68.61 - 85.76: 10 Dihedral angle restraints: 6618 sinusoidal: 2754 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS A 14 " pdb=" SG CYS A 14 " pdb=" SG CYS B 137 " pdb=" CB CYS B 137 " ideal model delta sinusoidal sigma weight residual -86.00 -158.43 72.43 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 56.33 36.67 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CA TRP C 84 " pdb=" C TRP C 84 " pdb=" N ASP C 85 " pdb=" CA ASP C 85 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1252 0.050 - 0.100: 291 0.100 - 0.150: 80 0.150 - 0.200: 23 0.200 - 0.250: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA CYS A 305 " pdb=" N CYS A 305 " pdb=" C CYS A 305 " pdb=" CB CYS A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA CYS E 305 " pdb=" N CYS E 305 " pdb=" C CYS E 305 " pdb=" CB CYS E 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA CYS C 305 " pdb=" N CYS C 305 " pdb=" C CYS C 305 " pdb=" CB CYS C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1647 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 190 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C GLU A 190 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 191 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 190 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C GLU E 190 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU E 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN E 191 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 190 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLU C 190 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU C 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN C 191 " 0.016 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 36 2.40 - 3.03: 6478 3.03 - 3.65: 16158 3.65 - 4.28: 23377 4.28 - 4.90: 38779 Nonbonded interactions: 84828 Sorted by model distance: nonbonded pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " model vdw 1.781 3.760 nonbonded pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " model vdw 1.789 3.760 nonbonded pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " model vdw 2.001 3.760 nonbonded pdb=" SG CYS E 64 " pdb=" SG CYS E 76 " model vdw 2.002 3.760 nonbonded pdb=" SG CYS E 97 " pdb=" SG CYS E 139 " model vdw 2.030 3.760 ... (remaining 84823 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.350 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.004 0.036 10824 Z= 0.256 Angle : 0.758 10.288 14685 Z= 0.435 Chirality : 0.051 0.250 1650 Planarity : 0.004 0.043 1917 Dihedral : 13.059 85.764 4110 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1323 helix: 0.39 (0.23), residues: 408 sheet: -0.52 (0.31), residues: 267 loop : -2.93 (0.17), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 222 HIS 0.002 0.001 HIS E 184 PHE 0.007 0.001 PHE A 79 TYR 0.012 0.002 TYR C 178 ARG 0.002 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.8238 (m-80) cc_final: 0.7727 (m-80) REVERT: B 58 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9094 (mttm) REVERT: B 64 HIS cc_start: 0.8925 (m-70) cc_final: 0.8573 (m-70) REVERT: B 65 GLN cc_start: 0.9440 (mm-40) cc_final: 0.8796 (tp-100) REVERT: B 66 ILE cc_start: 0.9717 (mt) cc_final: 0.9499 (mt) REVERT: B 69 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8491 (mt-10) REVERT: B 86 ASP cc_start: 0.8260 (t0) cc_final: 0.7850 (t0) REVERT: C 98 TYR cc_start: 0.8956 (t80) cc_final: 0.8240 (t80) REVERT: C 137 ASN cc_start: 0.9480 (m-40) cc_final: 0.9038 (p0) REVERT: E 50 LYS cc_start: 0.8581 (mttt) cc_final: 0.8120 (tptm) REVERT: E 87 PHE cc_start: 0.7100 (t80) cc_final: 0.6662 (t80) REVERT: E 98 TYR cc_start: 0.8297 (t80) cc_final: 0.7881 (t80) REVERT: E 233 TYR cc_start: 0.7983 (m-80) cc_final: 0.7715 (m-80) REVERT: D 39 LYS cc_start: 0.9733 (mptt) cc_final: 0.9515 (mmtm) REVERT: D 58 LYS cc_start: 0.9461 (mtmt) cc_final: 0.9051 (mttm) REVERT: D 62 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8598 (mmtt) REVERT: D 64 HIS cc_start: 0.8922 (m-70) cc_final: 0.8518 (m90) REVERT: D 86 ASP cc_start: 0.8450 (t0) cc_final: 0.8011 (t0) REVERT: D 108 ILE cc_start: 0.9723 (mt) cc_final: 0.9434 (tt) REVERT: F 38 LEU cc_start: 0.9521 (pt) cc_final: 0.9318 (pt) REVERT: F 39 LYS cc_start: 0.9736 (mptt) cc_final: 0.9515 (mmtm) REVERT: F 55 VAL cc_start: 0.9734 (m) cc_final: 0.9441 (m) REVERT: F 58 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9135 (mttm) REVERT: F 59 THR cc_start: 0.9595 (p) cc_final: 0.8865 (p) REVERT: F 63 PHE cc_start: 0.9340 (m-10) cc_final: 0.9002 (m-80) REVERT: F 64 HIS cc_start: 0.8930 (m-70) cc_final: 0.8520 (m90) REVERT: F 65 GLN cc_start: 0.9404 (mm-40) cc_final: 0.8907 (tp-100) REVERT: F 66 ILE cc_start: 0.9704 (mt) cc_final: 0.9377 (mt) REVERT: F 69 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8398 (mm-30) REVERT: F 70 PHE cc_start: 0.8781 (m-80) cc_final: 0.8220 (m-80) REVERT: F 78 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8497 (mm-40) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3266 time to fit residues: 116.3523 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.0970 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 184 HIS A 197 GLN A 216 ASN A 285 ASN A 298 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN C 184 HIS C 197 GLN C 216 ASN C 285 ASN C 298 ASN E 173 ASN E 184 HIS E 197 GLN E 216 ASN E 285 ASN D 64 HIS D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN D 159 HIS F 104 ASN F 146 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.085192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.056468 restraints weight = 46383.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.055915 restraints weight = 25077.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.056173 restraints weight = 21510.841| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10824 Z= 0.223 Angle : 0.578 7.584 14685 Z= 0.308 Chirality : 0.044 0.167 1650 Planarity : 0.004 0.053 1917 Dihedral : 5.036 37.580 1569 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.77 (0.21), residues: 1323 helix: 1.54 (0.24), residues: 399 sheet: 0.20 (0.34), residues: 246 loop : -2.18 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 127 HIS 0.008 0.002 HIS F 106 PHE 0.027 0.002 PHE B 70 TYR 0.017 0.002 TYR B 83 ARG 0.006 0.001 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.8817 (m-80) cc_final: 0.8544 (m-80) REVERT: A 137 ASN cc_start: 0.9459 (m-40) cc_final: 0.8693 (p0) REVERT: A 233 TYR cc_start: 0.8006 (m-80) cc_final: 0.7778 (m-80) REVERT: B 54 ARG cc_start: 0.9312 (mtp85) cc_final: 0.8686 (mtp85) REVERT: B 58 LYS cc_start: 0.9342 (mtmt) cc_final: 0.8801 (mttm) REVERT: B 61 GLU cc_start: 0.8894 (pp20) cc_final: 0.8384 (pp20) REVERT: B 62 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8603 (mmtt) REVERT: B 64 HIS cc_start: 0.8894 (m-70) cc_final: 0.8620 (m90) REVERT: B 86 ASP cc_start: 0.8693 (t0) cc_final: 0.8152 (t0) REVERT: B 117 LYS cc_start: 0.9830 (tptt) cc_final: 0.9620 (tptp) REVERT: B 133 MET cc_start: 0.7793 (ptt) cc_final: 0.7258 (ppp) REVERT: C 70 LEU cc_start: 0.8009 (tp) cc_final: 0.7596 (mt) REVERT: C 98 TYR cc_start: 0.8678 (t80) cc_final: 0.7987 (t80) REVERT: C 137 ASN cc_start: 0.9406 (m-40) cc_final: 0.8888 (p0) REVERT: C 184 HIS cc_start: 0.8021 (m-70) cc_final: 0.7678 (m90) REVERT: C 233 TYR cc_start: 0.7927 (m-80) cc_final: 0.7667 (m-80) REVERT: E 50 LYS cc_start: 0.8587 (mttt) cc_final: 0.8124 (tptm) REVERT: E 70 LEU cc_start: 0.8031 (tp) cc_final: 0.7742 (mt) REVERT: E 71 LEU cc_start: 0.9278 (mt) cc_final: 0.8808 (mt) REVERT: E 87 PHE cc_start: 0.6474 (t80) cc_final: 0.5795 (t80) REVERT: E 98 TYR cc_start: 0.8366 (t80) cc_final: 0.7728 (t80) REVERT: D 39 LYS cc_start: 0.9737 (mptt) cc_final: 0.9512 (mmtm) REVERT: D 58 LYS cc_start: 0.9419 (mtmt) cc_final: 0.8972 (mttm) REVERT: D 86 ASP cc_start: 0.8709 (t0) cc_final: 0.8177 (t0) REVERT: D 108 ILE cc_start: 0.9707 (mt) cc_final: 0.9507 (tt) REVERT: D 126 LEU cc_start: 0.9471 (tt) cc_final: 0.9257 (tt) REVERT: F 55 VAL cc_start: 0.9611 (m) cc_final: 0.9366 (m) REVERT: F 59 THR cc_start: 0.9534 (p) cc_final: 0.8745 (p) REVERT: F 63 PHE cc_start: 0.9259 (m-10) cc_final: 0.8903 (m-80) REVERT: F 86 ASP cc_start: 0.8712 (t0) cc_final: 0.8468 (t0) REVERT: F 117 LYS cc_start: 0.9803 (tptt) cc_final: 0.9597 (tptp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3186 time to fit residues: 88.1984 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 184 HIS B 64 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS D 64 HIS D 104 ASN F 64 HIS F 104 ASN ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.084739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.056166 restraints weight = 47110.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.056196 restraints weight = 24526.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.056074 restraints weight = 20841.831| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10824 Z= 0.170 Angle : 0.541 6.410 14685 Z= 0.289 Chirality : 0.044 0.152 1650 Planarity : 0.004 0.085 1917 Dihedral : 4.730 35.689 1569 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.38 (0.21), residues: 1323 helix: 1.69 (0.24), residues: 402 sheet: 0.34 (0.34), residues: 246 loop : -1.79 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 127 HIS 0.012 0.001 HIS D 64 PHE 0.019 0.002 PHE D 70 TYR 0.010 0.001 TYR B 83 ARG 0.009 0.001 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9446 (m-40) cc_final: 0.8698 (p0) REVERT: B 54 ARG cc_start: 0.9312 (mtp85) cc_final: 0.8611 (mtp-110) REVERT: B 58 LYS cc_start: 0.9396 (mtmt) cc_final: 0.9076 (mttm) REVERT: B 64 HIS cc_start: 0.8959 (m170) cc_final: 0.8528 (m-70) REVERT: B 86 ASP cc_start: 0.8837 (t0) cc_final: 0.8237 (t0) REVERT: B 118 LEU cc_start: 0.9681 (pp) cc_final: 0.9411 (pp) REVERT: B 133 MET cc_start: 0.7730 (ptt) cc_final: 0.7240 (ppp) REVERT: C 70 LEU cc_start: 0.8052 (tp) cc_final: 0.7637 (mt) REVERT: C 98 TYR cc_start: 0.8655 (t80) cc_final: 0.8124 (t80) REVERT: C 137 ASN cc_start: 0.9485 (m-40) cc_final: 0.8933 (p0) REVERT: C 233 TYR cc_start: 0.8274 (m-80) cc_final: 0.7745 (m-80) REVERT: E 50 LYS cc_start: 0.8544 (mttt) cc_final: 0.8110 (tptm) REVERT: E 71 LEU cc_start: 0.9223 (mt) cc_final: 0.8852 (mt) REVERT: E 98 TYR cc_start: 0.8143 (t80) cc_final: 0.7581 (t80) REVERT: E 233 TYR cc_start: 0.8268 (m-80) cc_final: 0.8068 (m-80) REVERT: D 54 ARG cc_start: 0.9330 (mtp85) cc_final: 0.8652 (mtp-110) REVERT: D 58 LYS cc_start: 0.9515 (mtmt) cc_final: 0.9219 (mttm) REVERT: D 62 LYS cc_start: 0.9337 (mmtt) cc_final: 0.8985 (mmmt) REVERT: D 86 ASP cc_start: 0.8762 (t0) cc_final: 0.8177 (t0) REVERT: D 108 ILE cc_start: 0.9699 (mt) cc_final: 0.9490 (tt) REVERT: D 133 MET cc_start: 0.7527 (ptt) cc_final: 0.7234 (ppp) REVERT: F 58 LYS cc_start: 0.9476 (ptpp) cc_final: 0.8833 (ptpt) REVERT: F 59 THR cc_start: 0.9579 (p) cc_final: 0.8697 (p) REVERT: F 61 GLU cc_start: 0.8973 (pp20) cc_final: 0.8152 (pp20) REVERT: F 62 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8642 (mmtt) REVERT: F 63 PHE cc_start: 0.9290 (m-10) cc_final: 0.8880 (m-80) REVERT: F 66 ILE cc_start: 0.9677 (mt) cc_final: 0.9412 (mt) REVERT: F 70 PHE cc_start: 0.8763 (m-80) cc_final: 0.8269 (m-80) REVERT: F 86 ASP cc_start: 0.8733 (t0) cc_final: 0.8265 (t0) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3068 time to fit residues: 79.9738 Evaluate side-chains 136 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 184 HIS D 104 ASN ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.087692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060508 restraints weight = 52411.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.058568 restraints weight = 29392.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058966 restraints weight = 27659.033| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10824 Z= 0.271 Angle : 0.599 6.578 14685 Z= 0.321 Chirality : 0.046 0.189 1650 Planarity : 0.004 0.043 1917 Dihedral : 5.404 46.083 1569 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.49 (0.21), residues: 1323 helix: 1.45 (0.24), residues: 402 sheet: 0.10 (0.32), residues: 261 loop : -1.70 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 127 HIS 0.005 0.001 HIS D 106 PHE 0.012 0.002 PHE F 70 TYR 0.018 0.002 TYR F 83 ARG 0.007 0.001 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9352 (m-40) cc_final: 0.8603 (p0) REVERT: A 190 GLU cc_start: 0.9018 (pt0) cc_final: 0.8744 (pt0) REVERT: A 233 TYR cc_start: 0.8379 (m-80) cc_final: 0.8082 (m-80) REVERT: B 51 LYS cc_start: 0.9414 (mmtt) cc_final: 0.9176 (mmtm) REVERT: B 54 ARG cc_start: 0.9084 (mtp85) cc_final: 0.8853 (mtp-110) REVERT: B 64 HIS cc_start: 0.8665 (m170) cc_final: 0.8359 (m-70) REVERT: B 68 LYS cc_start: 0.9316 (mmtm) cc_final: 0.9035 (mmtm) REVERT: B 86 ASP cc_start: 0.8392 (t0) cc_final: 0.7854 (t0) REVERT: B 90 ASP cc_start: 0.8877 (m-30) cc_final: 0.8640 (m-30) REVERT: B 133 MET cc_start: 0.7859 (ptt) cc_final: 0.7331 (ppp) REVERT: C 70 LEU cc_start: 0.7409 (tp) cc_final: 0.7023 (mt) REVERT: C 98 TYR cc_start: 0.8673 (t80) cc_final: 0.8177 (t80) REVERT: C 137 ASN cc_start: 0.9423 (m-40) cc_final: 0.8918 (p0) REVERT: C 231 SER cc_start: 0.8582 (m) cc_final: 0.7880 (m) REVERT: C 233 TYR cc_start: 0.8215 (m-80) cc_final: 0.7712 (m-80) REVERT: C 261 ARG cc_start: 0.5088 (mtt90) cc_final: 0.4027 (ptt90) REVERT: E 50 LYS cc_start: 0.8793 (mttt) cc_final: 0.8345 (tptm) REVERT: E 98 TYR cc_start: 0.8537 (t80) cc_final: 0.7966 (t80) REVERT: D 39 LYS cc_start: 0.9719 (mmtm) cc_final: 0.9510 (mmmt) REVERT: D 54 ARG cc_start: 0.9055 (mtp85) cc_final: 0.8538 (mtp-110) REVERT: D 58 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9121 (mttm) REVERT: D 62 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8882 (mmmt) REVERT: D 86 ASP cc_start: 0.8435 (t0) cc_final: 0.7929 (t0) REVERT: D 90 ASP cc_start: 0.8782 (m-30) cc_final: 0.8491 (m-30) REVERT: D 133 MET cc_start: 0.7647 (ptt) cc_final: 0.7392 (ppp) REVERT: F 59 THR cc_start: 0.9388 (p) cc_final: 0.8403 (p) REVERT: F 63 PHE cc_start: 0.9163 (m-10) cc_final: 0.8880 (m-80) REVERT: F 66 ILE cc_start: 0.9617 (mt) cc_final: 0.9318 (mt) REVERT: F 70 PHE cc_start: 0.8492 (m-80) cc_final: 0.8112 (m-80) REVERT: F 86 ASP cc_start: 0.8375 (t0) cc_final: 0.7843 (t0) REVERT: F 90 ASP cc_start: 0.9045 (m-30) cc_final: 0.8827 (m-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3049 time to fit residues: 77.8142 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 116 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN B 159 HIS C 184 HIS E 184 HIS E 298 ASN D 60 ASN D 78 GLN D 104 ASN D 125 GLN F 104 ASN ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.086371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053960 restraints weight = 52667.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.056136 restraints weight = 27817.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.057358 restraints weight = 19587.514| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10824 Z= 0.300 Angle : 0.619 6.813 14685 Z= 0.331 Chirality : 0.045 0.189 1650 Planarity : 0.004 0.038 1917 Dihedral : 5.402 41.807 1569 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.08 % Allowed : 2.44 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.72 (0.21), residues: 1323 helix: 1.24 (0.25), residues: 399 sheet: -0.14 (0.34), residues: 228 loop : -1.69 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 127 HIS 0.009 0.001 HIS F 106 PHE 0.013 0.002 PHE C 120 TYR 0.017 0.002 TYR B 83 ARG 0.009 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7928 (t80) cc_final: 0.7601 (t80) REVERT: A 137 ASN cc_start: 0.9353 (m-40) cc_final: 0.8643 (p0) REVERT: A 231 SER cc_start: 0.8738 (t) cc_final: 0.8523 (t) REVERT: A 233 TYR cc_start: 0.8292 (m-80) cc_final: 0.7870 (m-80) REVERT: B 58 LYS cc_start: 0.9319 (mtmt) cc_final: 0.8802 (mttm) REVERT: B 62 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8969 (mmtt) REVERT: B 64 HIS cc_start: 0.8729 (m170) cc_final: 0.8408 (m90) REVERT: B 86 ASP cc_start: 0.7933 (t0) cc_final: 0.7572 (t0) REVERT: B 133 MET cc_start: 0.7816 (ptt) cc_final: 0.7322 (ppp) REVERT: C 70 LEU cc_start: 0.7592 (tp) cc_final: 0.7158 (mt) REVERT: C 98 TYR cc_start: 0.8794 (t80) cc_final: 0.8252 (t80) REVERT: C 231 SER cc_start: 0.8636 (m) cc_final: 0.8069 (m) REVERT: C 233 TYR cc_start: 0.8355 (m-80) cc_final: 0.7906 (m-80) REVERT: E 50 LYS cc_start: 0.8900 (mttt) cc_final: 0.8471 (tptm) REVERT: E 98 TYR cc_start: 0.8711 (t80) cc_final: 0.8145 (t80) REVERT: D 51 LYS cc_start: 0.9501 (mmtt) cc_final: 0.8974 (mmtp) REVERT: D 54 ARG cc_start: 0.9134 (mtp85) cc_final: 0.8735 (mtm110) REVERT: D 58 LYS cc_start: 0.9458 (mtmt) cc_final: 0.9205 (mttm) REVERT: D 62 LYS cc_start: 0.9353 (mmtt) cc_final: 0.9010 (mmmt) REVERT: D 63 PHE cc_start: 0.9167 (m-10) cc_final: 0.8877 (m-80) REVERT: D 67 GLU cc_start: 0.9236 (pt0) cc_final: 0.8717 (pp20) REVERT: D 86 ASP cc_start: 0.7986 (t0) cc_final: 0.7614 (t0) REVERT: D 114 GLU cc_start: 0.9165 (pp20) cc_final: 0.8854 (pp20) REVERT: D 133 MET cc_start: 0.7548 (ptt) cc_final: 0.7186 (ppp) REVERT: F 59 THR cc_start: 0.9431 (p) cc_final: 0.8674 (p) REVERT: F 63 PHE cc_start: 0.9208 (m-10) cc_final: 0.8883 (m-80) REVERT: F 66 ILE cc_start: 0.9665 (mt) cc_final: 0.9324 (mt) REVERT: F 70 PHE cc_start: 0.8505 (m-80) cc_final: 0.8117 (m-80) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.2948 time to fit residues: 71.8872 Evaluate side-chains 136 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 105 GLN E 184 HIS D 60 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN F 159 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.088441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.062699 restraints weight = 52204.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.060609 restraints weight = 30659.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.060888 restraints weight = 32417.137| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10824 Z= 0.180 Angle : 0.577 11.582 14685 Z= 0.303 Chirality : 0.045 0.163 1650 Planarity : 0.004 0.044 1917 Dihedral : 4.859 34.941 1569 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.38 (0.22), residues: 1323 helix: 1.66 (0.25), residues: 399 sheet: 0.00 (0.34), residues: 228 loop : -1.56 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 127 HIS 0.017 0.001 HIS B 159 PHE 0.014 0.001 PHE B 63 TYR 0.009 0.001 TYR B 157 ARG 0.008 0.000 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7981 (t80) cc_final: 0.7673 (t80) REVERT: A 137 ASN cc_start: 0.9232 (m-40) cc_final: 0.8430 (p0) REVERT: A 320 MET cc_start: 0.5153 (ptm) cc_final: 0.4926 (ptp) REVERT: B 54 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8542 (mtp-110) REVERT: B 58 LYS cc_start: 0.9280 (mtmt) cc_final: 0.8619 (mttm) REVERT: B 61 GLU cc_start: 0.8714 (pp20) cc_final: 0.8324 (pp20) REVERT: B 64 HIS cc_start: 0.8695 (m170) cc_final: 0.8311 (m90) REVERT: B 66 ILE cc_start: 0.9642 (mt) cc_final: 0.9157 (mt) REVERT: B 70 PHE cc_start: 0.8473 (m-80) cc_final: 0.7135 (m-80) REVERT: B 86 ASP cc_start: 0.8579 (t0) cc_final: 0.7918 (t0) REVERT: B 90 ASP cc_start: 0.8956 (m-30) cc_final: 0.8731 (m-30) REVERT: B 111 THR cc_start: 0.8993 (t) cc_final: 0.8684 (t) REVERT: B 133 MET cc_start: 0.7836 (ptt) cc_final: 0.7316 (ppp) REVERT: C 70 LEU cc_start: 0.7503 (tp) cc_final: 0.7171 (mt) REVERT: C 98 TYR cc_start: 0.8673 (t80) cc_final: 0.8202 (t80) REVERT: C 231 SER cc_start: 0.8442 (m) cc_final: 0.7767 (m) REVERT: C 233 TYR cc_start: 0.8149 (m-80) cc_final: 0.7783 (m-80) REVERT: E 50 LYS cc_start: 0.8795 (mttt) cc_final: 0.8350 (tptm) REVERT: E 98 TYR cc_start: 0.8556 (t80) cc_final: 0.7934 (t80) REVERT: D 54 ARG cc_start: 0.9060 (mtp85) cc_final: 0.8567 (mtp-110) REVERT: D 58 LYS cc_start: 0.9419 (mtmt) cc_final: 0.9102 (mttm) REVERT: D 59 THR cc_start: 0.9363 (p) cc_final: 0.8624 (p) REVERT: D 62 LYS cc_start: 0.9281 (mmtt) cc_final: 0.9002 (mmtt) REVERT: D 63 PHE cc_start: 0.9057 (m-10) cc_final: 0.8840 (m-80) REVERT: D 86 ASP cc_start: 0.8457 (t0) cc_final: 0.7848 (t0) REVERT: D 133 MET cc_start: 0.7654 (ptt) cc_final: 0.7323 (ppp) REVERT: F 39 LYS cc_start: 0.9731 (mmtm) cc_final: 0.9505 (mmmt) REVERT: F 59 THR cc_start: 0.9416 (p) cc_final: 0.8673 (p) REVERT: F 62 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8934 (ptpp) REVERT: F 63 PHE cc_start: 0.9154 (m-10) cc_final: 0.8809 (m-80) REVERT: F 66 ILE cc_start: 0.9615 (mt) cc_final: 0.9060 (mt) REVERT: F 70 PHE cc_start: 0.8536 (m-80) cc_final: 0.7904 (m-80) REVERT: F 86 ASP cc_start: 0.8569 (t0) cc_final: 0.7898 (t0) REVERT: F 90 ASP cc_start: 0.8968 (m-30) cc_final: 0.8755 (m-30) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3066 time to fit residues: 75.6908 Evaluate side-chains 142 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 96 optimal weight: 0.0870 chunk 106 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN C 184 HIS E 184 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.089524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.062368 restraints weight = 52244.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060357 restraints weight = 28172.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.060883 restraints weight = 25948.559| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10824 Z= 0.153 Angle : 0.573 10.683 14685 Z= 0.298 Chirality : 0.044 0.160 1650 Planarity : 0.004 0.044 1917 Dihedral : 4.467 34.540 1569 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.11 (0.22), residues: 1323 helix: 1.74 (0.25), residues: 396 sheet: 0.03 (0.36), residues: 192 loop : -1.17 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 127 HIS 0.013 0.001 HIS B 159 PHE 0.029 0.001 PHE B 70 TYR 0.007 0.001 TYR A 302 ARG 0.006 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8132 (t80) cc_final: 0.7733 (t80) REVERT: A 137 ASN cc_start: 0.9301 (m-40) cc_final: 0.8570 (p0) REVERT: B 58 LYS cc_start: 0.9291 (mtmt) cc_final: 0.8848 (mttm) REVERT: B 59 THR cc_start: 0.9506 (p) cc_final: 0.8766 (p) REVERT: B 62 LYS cc_start: 0.9257 (mmtt) cc_final: 0.8908 (mmtt) REVERT: B 64 HIS cc_start: 0.8662 (m170) cc_final: 0.8203 (m90) REVERT: B 65 GLN cc_start: 0.8810 (pm20) cc_final: 0.8584 (pm20) REVERT: B 86 ASP cc_start: 0.8423 (t0) cc_final: 0.7877 (t0) REVERT: B 90 ASP cc_start: 0.8967 (m-30) cc_final: 0.8702 (m-30) REVERT: B 133 MET cc_start: 0.7852 (ptt) cc_final: 0.7384 (ppp) REVERT: C 70 LEU cc_start: 0.7567 (tp) cc_final: 0.7202 (mt) REVERT: C 98 TYR cc_start: 0.8791 (t80) cc_final: 0.8183 (t80) REVERT: C 184 HIS cc_start: 0.7966 (m-70) cc_final: 0.7738 (m-70) REVERT: C 231 SER cc_start: 0.8415 (m) cc_final: 0.7773 (m) REVERT: C 233 TYR cc_start: 0.8197 (m-80) cc_final: 0.7828 (m-80) REVERT: C 261 ARG cc_start: 0.4688 (mtt90) cc_final: 0.3143 (ppt170) REVERT: E 50 LYS cc_start: 0.8733 (mttt) cc_final: 0.8280 (tptm) REVERT: E 98 TYR cc_start: 0.8648 (t80) cc_final: 0.7989 (t80) REVERT: D 64 HIS cc_start: 0.8606 (m170) cc_final: 0.8320 (m-70) REVERT: D 86 ASP cc_start: 0.8364 (t0) cc_final: 0.7789 (t0) REVERT: D 90 ASP cc_start: 0.8849 (m-30) cc_final: 0.8635 (m-30) REVERT: D 133 MET cc_start: 0.7740 (ptt) cc_final: 0.7428 (ppp) REVERT: F 39 LYS cc_start: 0.9739 (mmtm) cc_final: 0.9528 (mmmt) REVERT: F 59 THR cc_start: 0.9354 (p) cc_final: 0.8625 (p) REVERT: F 63 PHE cc_start: 0.9131 (m-10) cc_final: 0.8913 (m-80) REVERT: F 64 HIS cc_start: 0.8641 (m170) cc_final: 0.7944 (m90) REVERT: F 68 LYS cc_start: 0.8915 (mmtm) cc_final: 0.8694 (mmtt) REVERT: F 86 ASP cc_start: 0.8369 (t0) cc_final: 0.7756 (t0) REVERT: F 90 ASP cc_start: 0.9042 (m-30) cc_final: 0.8777 (m-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2916 time to fit residues: 70.1860 Evaluate side-chains 144 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 104 ASN E 184 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.088684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.061988 restraints weight = 51771.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.059891 restraints weight = 27305.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060376 restraints weight = 26297.843| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10824 Z= 0.191 Angle : 0.589 10.087 14685 Z= 0.311 Chirality : 0.045 0.163 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.632 46.288 1569 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.12 (0.22), residues: 1323 helix: 1.69 (0.25), residues: 405 sheet: 0.05 (0.36), residues: 192 loop : -1.19 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 127 HIS 0.011 0.001 HIS B 159 PHE 0.059 0.002 PHE B 70 TYR 0.007 0.001 TYR F 83 ARG 0.005 0.000 ARG D 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8170 (t80) cc_final: 0.7752 (t80) REVERT: A 137 ASN cc_start: 0.9293 (m-40) cc_final: 0.8565 (p0) REVERT: A 280 GLU cc_start: 0.8877 (mp0) cc_final: 0.8481 (pm20) REVERT: A 288 ILE cc_start: 0.8862 (mp) cc_final: 0.8382 (mp) REVERT: B 54 ARG cc_start: 0.9051 (mtp85) cc_final: 0.8514 (ptm-80) REVERT: B 58 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8769 (mttm) REVERT: B 59 THR cc_start: 0.9485 (p) cc_final: 0.8814 (p) REVERT: B 63 PHE cc_start: 0.8802 (m-10) cc_final: 0.8564 (m-80) REVERT: B 64 HIS cc_start: 0.8631 (m170) cc_final: 0.8203 (m-70) REVERT: B 65 GLN cc_start: 0.8929 (pm20) cc_final: 0.8574 (pm20) REVERT: B 86 ASP cc_start: 0.8418 (t0) cc_final: 0.7896 (t0) REVERT: B 90 ASP cc_start: 0.8975 (m-30) cc_final: 0.8729 (m-30) REVERT: B 123 ARG cc_start: 0.9273 (pmt-80) cc_final: 0.9017 (pmt-80) REVERT: B 133 MET cc_start: 0.7829 (ptt) cc_final: 0.7345 (ppp) REVERT: C 70 LEU cc_start: 0.7535 (tp) cc_final: 0.7269 (mt) REVERT: C 98 TYR cc_start: 0.8785 (t80) cc_final: 0.8193 (t80) REVERT: C 233 TYR cc_start: 0.8182 (m-80) cc_final: 0.7847 (m-80) REVERT: E 50 LYS cc_start: 0.8741 (mttt) cc_final: 0.8266 (tptm) REVERT: E 98 TYR cc_start: 0.8667 (t80) cc_final: 0.8031 (t80) REVERT: D 59 THR cc_start: 0.9319 (p) cc_final: 0.8649 (p) REVERT: D 64 HIS cc_start: 0.8640 (m170) cc_final: 0.8337 (m-70) REVERT: D 86 ASP cc_start: 0.8396 (t0) cc_final: 0.7859 (t0) REVERT: D 90 ASP cc_start: 0.8872 (m-30) cc_final: 0.8659 (m-30) REVERT: D 133 MET cc_start: 0.7744 (ptt) cc_final: 0.7434 (ppp) REVERT: F 39 LYS cc_start: 0.9719 (mmtm) cc_final: 0.9495 (mmmt) REVERT: F 59 THR cc_start: 0.9508 (p) cc_final: 0.8616 (p) REVERT: F 63 PHE cc_start: 0.9205 (m-10) cc_final: 0.8971 (m-80) REVERT: F 64 HIS cc_start: 0.8568 (m170) cc_final: 0.8098 (m90) REVERT: F 66 ILE cc_start: 0.9556 (mt) cc_final: 0.8938 (mt) REVERT: F 70 PHE cc_start: 0.8226 (m-80) cc_final: 0.7796 (m-80) REVERT: F 86 ASP cc_start: 0.8355 (t0) cc_final: 0.7753 (t0) REVERT: F 90 ASP cc_start: 0.9027 (m-30) cc_final: 0.8768 (m-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3055 time to fit residues: 72.1366 Evaluate side-chains 140 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 113 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.087841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.061715 restraints weight = 52789.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.059480 restraints weight = 29131.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060147 restraints weight = 27062.659| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10824 Z= 0.228 Angle : 0.598 9.363 14685 Z= 0.319 Chirality : 0.045 0.178 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.728 35.819 1569 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.12 (0.22), residues: 1323 helix: 1.70 (0.25), residues: 405 sheet: -0.05 (0.34), residues: 234 loop : -1.23 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 127 HIS 0.011 0.001 HIS B 159 PHE 0.048 0.002 PHE B 70 TYR 0.010 0.001 TYR F 83 ARG 0.005 0.000 ARG D 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8213 (t80) cc_final: 0.7757 (t80) REVERT: A 137 ASN cc_start: 0.9249 (m-40) cc_final: 0.8469 (p0) REVERT: B 59 THR cc_start: 0.9393 (p) cc_final: 0.8606 (p) REVERT: B 63 PHE cc_start: 0.8818 (m-10) cc_final: 0.8569 (m-80) REVERT: B 64 HIS cc_start: 0.8675 (m170) cc_final: 0.8271 (m-70) REVERT: B 65 GLN cc_start: 0.8870 (pm20) cc_final: 0.8502 (pm20) REVERT: B 86 ASP cc_start: 0.8375 (t0) cc_final: 0.7871 (t0) REVERT: B 90 ASP cc_start: 0.8982 (m-30) cc_final: 0.8713 (m-30) REVERT: B 133 MET cc_start: 0.7884 (ptt) cc_final: 0.7413 (ppp) REVERT: C 70 LEU cc_start: 0.7579 (tp) cc_final: 0.7279 (mt) REVERT: C 98 TYR cc_start: 0.8721 (t80) cc_final: 0.8190 (t80) REVERT: C 231 SER cc_start: 0.8431 (m) cc_final: 0.7661 (m) REVERT: C 233 TYR cc_start: 0.8195 (m-80) cc_final: 0.7871 (m-80) REVERT: E 98 TYR cc_start: 0.8638 (t80) cc_final: 0.8012 (t80) REVERT: D 64 HIS cc_start: 0.8591 (m170) cc_final: 0.8189 (m-70) REVERT: D 86 ASP cc_start: 0.8329 (t0) cc_final: 0.7773 (t0) REVERT: D 90 ASP cc_start: 0.8772 (m-30) cc_final: 0.8441 (m-30) REVERT: D 114 GLU cc_start: 0.9183 (pp20) cc_final: 0.8973 (pp20) REVERT: D 115 MET cc_start: 0.8781 (tpt) cc_final: 0.8580 (tpt) REVERT: D 117 LYS cc_start: 0.9787 (tmmt) cc_final: 0.9518 (tmtt) REVERT: D 133 MET cc_start: 0.7638 (ptt) cc_final: 0.7341 (ppp) REVERT: F 39 LYS cc_start: 0.9708 (mmtm) cc_final: 0.9487 (mmmt) REVERT: F 64 HIS cc_start: 0.8545 (m170) cc_final: 0.8024 (m90) REVERT: F 86 ASP cc_start: 0.8274 (t0) cc_final: 0.7690 (t0) REVERT: F 90 ASP cc_start: 0.8996 (m-30) cc_final: 0.8748 (m-30) REVERT: F 133 MET cc_start: 0.7805 (ptt) cc_final: 0.7498 (mpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2860 time to fit residues: 65.3367 Evaluate side-chains 134 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.088158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.062207 restraints weight = 51831.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.059813 restraints weight = 31984.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060163 restraints weight = 31817.013| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10824 Z= 0.205 Angle : 0.591 9.560 14685 Z= 0.314 Chirality : 0.045 0.178 1650 Planarity : 0.004 0.039 1917 Dihedral : 4.516 34.250 1569 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.06 (0.22), residues: 1323 helix: 1.77 (0.25), residues: 405 sheet: -0.02 (0.34), residues: 234 loop : -1.20 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 127 HIS 0.009 0.001 HIS B 159 PHE 0.040 0.002 PHE B 70 TYR 0.009 0.001 TYR D 83 ARG 0.005 0.000 ARG D 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8290 (t80) cc_final: 0.7795 (t80) REVERT: A 137 ASN cc_start: 0.9310 (m-40) cc_final: 0.8531 (p0) REVERT: A 280 GLU cc_start: 0.8970 (mp0) cc_final: 0.8674 (mp0) REVERT: B 54 ARG cc_start: 0.8994 (mtp85) cc_final: 0.8429 (mtp-110) REVERT: B 58 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8920 (mttm) REVERT: B 64 HIS cc_start: 0.8672 (m170) cc_final: 0.8307 (m-70) REVERT: B 65 GLN cc_start: 0.8883 (pm20) cc_final: 0.8499 (pm20) REVERT: B 86 ASP cc_start: 0.8487 (t0) cc_final: 0.7959 (t0) REVERT: B 90 ASP cc_start: 0.8990 (m-30) cc_final: 0.8720 (m-30) REVERT: B 133 MET cc_start: 0.7889 (ptt) cc_final: 0.7485 (ppp) REVERT: C 70 LEU cc_start: 0.7518 (tp) cc_final: 0.7211 (mt) REVERT: C 98 TYR cc_start: 0.8739 (t80) cc_final: 0.8205 (t80) REVERT: C 233 TYR cc_start: 0.8214 (m-80) cc_final: 0.7906 (m-80) REVERT: E 98 TYR cc_start: 0.8631 (t80) cc_final: 0.7996 (t80) REVERT: D 63 PHE cc_start: 0.8982 (m-10) cc_final: 0.8771 (m-80) REVERT: D 64 HIS cc_start: 0.8597 (m170) cc_final: 0.8202 (m-70) REVERT: D 86 ASP cc_start: 0.8426 (t0) cc_final: 0.7855 (t0) REVERT: D 90 ASP cc_start: 0.8895 (m-30) cc_final: 0.8692 (m-30) REVERT: D 114 GLU cc_start: 0.9217 (pp20) cc_final: 0.8949 (pp20) REVERT: D 115 MET cc_start: 0.8874 (tpt) cc_final: 0.8634 (tpt) REVERT: D 133 MET cc_start: 0.7625 (ptt) cc_final: 0.7370 (ppp) REVERT: F 39 LYS cc_start: 0.9712 (mmtm) cc_final: 0.9511 (mmmt) REVERT: F 62 LYS cc_start: 0.9262 (ptpp) cc_final: 0.9028 (ptpp) REVERT: F 64 HIS cc_start: 0.8573 (m170) cc_final: 0.8033 (m90) REVERT: F 86 ASP cc_start: 0.8457 (t0) cc_final: 0.7842 (t0) REVERT: F 90 ASP cc_start: 0.9032 (m-30) cc_final: 0.8815 (m-30) REVERT: F 133 MET cc_start: 0.7770 (ptt) cc_final: 0.7506 (mpp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2845 time to fit residues: 65.7875 Evaluate side-chains 138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN D 60 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.078220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047085 restraints weight = 48661.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.049555 restraints weight = 23513.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.050928 restraints weight = 15376.822| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 10824 Z= 0.475 Angle : 0.784 9.300 14685 Z= 0.420 Chirality : 0.052 0.223 1650 Planarity : 0.005 0.048 1917 Dihedral : 5.942 49.109 1569 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1323 helix: 0.86 (0.24), residues: 405 sheet: -0.66 (0.31), residues: 252 loop : -1.72 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 127 HIS 0.014 0.002 HIS B 159 PHE 0.052 0.003 PHE B 70 TYR 0.021 0.003 TYR B 83 ARG 0.005 0.001 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.46 seconds wall clock time: 73 minutes 56.59 seconds (4436.59 seconds total)