Starting phenix.real_space_refine on Sun Dec 29 15:18:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5k_10700/12_2024/6y5k_10700.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5k_10700/12_2024/6y5k_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_10700/12_2024/6y5k_10700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5k_10700/12_2024/6y5k_10700.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5k_10700/12_2024/6y5k_10700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5k_10700/12_2024/6y5k_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-5532/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: 6.70, per 1000 atoms: 0.63 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 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: 1.61 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: 3.60 Time building geometry restraints manager: 3.19 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.460 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- 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 : 1.291 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: 0.3257 time to fit residues: 116.2008 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 : 1.267 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 1.393 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: 0.8778 (m-80) cc_final: 0.8492 (m-80) REVERT: A 137 ASN cc_start: 0.9496 (m-40) cc_final: 0.8804 (p0) REVERT: A 233 TYR cc_start: 0.8133 (m-80) cc_final: 0.7844 (m-80) REVERT: B 54 ARG cc_start: 0.9472 (mtp85) cc_final: 0.8842 (mtp85) REVERT: B 58 LYS cc_start: 0.9378 (mtmt) cc_final: 0.8858 (mttm) REVERT: B 61 GLU cc_start: 0.8998 (pp20) cc_final: 0.8562 (pp20) REVERT: B 62 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8596 (mmtt) REVERT: B 64 HIS cc_start: 0.8970 (m-70) cc_final: 0.8687 (m90) REVERT: B 86 ASP cc_start: 0.8483 (t0) cc_final: 0.7956 (t0) REVERT: B 117 LYS cc_start: 0.9812 (tptt) cc_final: 0.9606 (tptp) REVERT: B 133 MET cc_start: 0.7694 (ptt) cc_final: 0.7161 (ppp) REVERT: C 70 LEU cc_start: 0.8023 (tp) cc_final: 0.7610 (mt) REVERT: C 98 TYR cc_start: 0.8711 (t80) cc_final: 0.7967 (t80) REVERT: C 137 ASN cc_start: 0.9497 (m-40) cc_final: 0.9053 (p0) REVERT: C 184 HIS cc_start: 0.8024 (m-70) cc_final: 0.7736 (m90) REVERT: C 233 TYR cc_start: 0.8013 (m-80) cc_final: 0.7699 (m-80) REVERT: E 50 LYS cc_start: 0.8533 (mttt) cc_final: 0.8067 (tptm) REVERT: E 70 LEU cc_start: 0.8036 (tp) cc_final: 0.7745 (mt) REVERT: E 71 LEU cc_start: 0.9306 (mt) cc_final: 0.8842 (mt) REVERT: E 87 PHE cc_start: 0.6242 (t80) cc_final: 0.5595 (t80) REVERT: E 98 TYR cc_start: 0.8362 (t80) cc_final: 0.7721 (t80) REVERT: D 39 LYS cc_start: 0.9723 (mptt) cc_final: 0.9489 (mmtm) REVERT: D 58 LYS cc_start: 0.9450 (mtmt) cc_final: 0.9021 (mttm) REVERT: D 86 ASP cc_start: 0.8520 (t0) cc_final: 0.7991 (t0) REVERT: D 126 LEU cc_start: 0.9440 (tt) cc_final: 0.9234 (tt) REVERT: F 55 VAL cc_start: 0.9738 (m) cc_final: 0.9502 (m) REVERT: F 59 THR cc_start: 0.9623 (p) cc_final: 0.8939 (p) REVERT: F 63 PHE cc_start: 0.9375 (m-10) cc_final: 0.9016 (m-80) REVERT: F 86 ASP cc_start: 0.8434 (t0) cc_final: 0.8193 (t0) REVERT: F 117 LYS cc_start: 0.9778 (tptt) cc_final: 0.9564 (tptp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3195 time to fit residues: 88.9875 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 : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 104 ASN B 105 GLN ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS D 64 HIS D 104 ASN F 64 HIS ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN F 159 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10824 Z= 0.191 Angle : 0.549 6.234 14685 Z= 0.294 Chirality : 0.044 0.158 1650 Planarity : 0.004 0.055 1917 Dihedral : 4.821 37.651 1569 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -0.43 (0.21), residues: 1323 helix: 1.63 (0.24), residues: 402 sheet: 0.31 (0.34), residues: 246 loop : -1.81 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 127 HIS 0.011 0.001 HIS D 64 PHE 0.017 0.002 PHE D 70 TYR 0.012 0.001 TYR B 83 ARG 0.008 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 198 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.379 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 137 ASN cc_start: 0.9475 (m-40) cc_final: 0.8793 (p0) REVERT: A 233 TYR cc_start: 0.8100 (m-80) cc_final: 0.7867 (m-80) REVERT: B 54 ARG cc_start: 0.9472 (mtp85) cc_final: 0.8978 (mtp-110) REVERT: B 64 HIS cc_start: 0.9047 (m170) cc_final: 0.8641 (m-70) REVERT: B 86 ASP cc_start: 0.8530 (t0) cc_final: 0.7967 (t0) REVERT: B 118 LEU cc_start: 0.9676 (pp) cc_final: 0.9391 (pp) REVERT: B 133 MET cc_start: 0.7613 (ptt) cc_final: 0.7113 (ppp) REVERT: C 70 LEU cc_start: 0.7936 (tp) cc_final: 0.7548 (mt) REVERT: C 98 TYR cc_start: 0.8698 (t80) cc_final: 0.8135 (t80) REVERT: C 137 ASN cc_start: 0.9554 (m-40) cc_final: 0.9060 (p0) REVERT: C 233 TYR cc_start: 0.8326 (m-80) cc_final: 0.7782 (m-80) REVERT: E 50 LYS cc_start: 0.8527 (mttt) cc_final: 0.8078 (tptm) REVERT: E 70 LEU cc_start: 0.8020 (tp) cc_final: 0.7791 (mt) REVERT: E 71 LEU cc_start: 0.9227 (mt) cc_final: 0.8891 (mt) REVERT: E 98 TYR cc_start: 0.8131 (t80) cc_final: 0.7595 (t80) REVERT: E 233 TYR cc_start: 0.8356 (m-80) cc_final: 0.8112 (m-80) REVERT: D 54 ARG cc_start: 0.9489 (mtp85) cc_final: 0.8795 (mtp-110) REVERT: D 58 LYS cc_start: 0.9556 (mtmt) cc_final: 0.9273 (mttm) REVERT: D 61 GLU cc_start: 0.9089 (pp20) cc_final: 0.8884 (pp20) REVERT: D 62 LYS cc_start: 0.9315 (mmtt) cc_final: 0.9012 (mmmt) REVERT: D 86 ASP cc_start: 0.8553 (t0) cc_final: 0.7989 (t0) REVERT: D 133 MET cc_start: 0.7431 (ptt) cc_final: 0.7156 (ppp) REVERT: F 58 LYS cc_start: 0.9520 (ptpp) cc_final: 0.8896 (ptpt) REVERT: F 59 THR cc_start: 0.9652 (p) cc_final: 0.8874 (p) REVERT: F 61 GLU cc_start: 0.9092 (pp20) cc_final: 0.8647 (pp20) REVERT: F 62 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8793 (mmtt) REVERT: F 63 PHE cc_start: 0.9413 (m-10) cc_final: 0.9054 (m-80) REVERT: F 66 ILE cc_start: 0.9701 (mt) cc_final: 0.9428 (mt) REVERT: F 70 PHE cc_start: 0.8757 (m-80) cc_final: 0.8271 (m-80) REVERT: F 86 ASP cc_start: 0.8442 (t0) cc_final: 0.7978 (t0) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3069 time to fit residues: 79.8302 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 : 1.349 ------------------------------------------------------------------------------- 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: 0.0670 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.0170 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.5972 ------------------------------------------------------------------------------- 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 159 HIS C 184 HIS E 184 HIS E 298 ASN D 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10824 Z= 0.158 Angle : 0.541 7.548 14685 Z= 0.287 Chirality : 0.044 0.154 1650 Planarity : 0.004 0.054 1917 Dihedral : 4.711 35.547 1569 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: -0.24 (0.22), residues: 1323 helix: 1.71 (0.25), residues: 402 sheet: 0.37 (0.34), residues: 246 loop : -1.62 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 127 HIS 0.008 0.001 HIS D 106 PHE 0.013 0.001 PHE C 258 TYR 0.008 0.001 TYR F 83 ARG 0.008 0.000 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 198 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.396 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: 0.9402 (m-40) cc_final: 0.8773 (p0) REVERT: A 233 TYR cc_start: 0.8119 (m-80) cc_final: 0.7822 (m-80) REVERT: A 288 ILE cc_start: 0.9269 (mt) cc_final: 0.9050 (mt) REVERT: B 54 ARG cc_start: 0.9480 (mtp85) cc_final: 0.9003 (mtp-110) REVERT: B 64 HIS cc_start: 0.9002 (m170) cc_final: 0.8489 (m-70) REVERT: B 68 LYS cc_start: 0.9436 (mmtm) cc_final: 0.9109 (mmtm) REVERT: B 86 ASP cc_start: 0.8525 (t0) cc_final: 0.7915 (t0) REVERT: B 133 MET cc_start: 0.7680 (ptt) cc_final: 0.7161 (ppp) REVERT: C 70 LEU cc_start: 0.7666 (tp) cc_final: 0.7338 (mt) REVERT: C 98 TYR cc_start: 0.8738 (t80) cc_final: 0.8156 (t80) REVERT: C 100 TYR cc_start: 0.7514 (p90) cc_final: 0.7207 (p90) REVERT: C 137 ASN cc_start: 0.9516 (m-40) cc_final: 0.9095 (p0) REVERT: C 233 TYR cc_start: 0.8290 (m-80) cc_final: 0.7735 (m-80) REVERT: C 261 ARG cc_start: 0.5045 (mtt90) cc_final: 0.4326 (ptt90) REVERT: E 50 LYS cc_start: 0.8506 (mttt) cc_final: 0.8066 (tptp) REVERT: E 71 LEU cc_start: 0.9323 (mt) cc_final: 0.8869 (mt) REVERT: E 98 TYR cc_start: 0.8359 (t80) cc_final: 0.7594 (t80) REVERT: D 39 LYS cc_start: 0.9737 (mmtm) cc_final: 0.9478 (mmmt) REVERT: D 42 GLN cc_start: 0.9624 (mt0) cc_final: 0.9305 (mt0) REVERT: D 54 ARG cc_start: 0.9467 (mtp85) cc_final: 0.8785 (mtp-110) REVERT: D 58 LYS cc_start: 0.9569 (mtmt) cc_final: 0.9302 (mttm) REVERT: D 86 ASP cc_start: 0.8554 (t0) cc_final: 0.7954 (t0) REVERT: D 133 MET cc_start: 0.7362 (ptt) cc_final: 0.7131 (ppp) REVERT: F 59 THR cc_start: 0.9658 (p) cc_final: 0.9015 (p) REVERT: F 61 GLU cc_start: 0.9115 (pp20) cc_final: 0.8730 (pp20) REVERT: F 62 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8785 (mmtt) REVERT: F 63 PHE cc_start: 0.9418 (m-10) cc_final: 0.9167 (m-80) REVERT: F 66 ILE cc_start: 0.9709 (mt) cc_final: 0.9424 (mt) REVERT: F 70 PHE cc_start: 0.8750 (m-80) cc_final: 0.8257 (m-80) REVERT: F 86 ASP cc_start: 0.8468 (t0) cc_final: 0.7848 (t0) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2959 time to fit residues: 77.0076 Evaluate side-chains 130 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 60 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN C 216 ASN E 184 HIS D 104 ASN F 104 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10824 Z= 0.299 Angle : 0.613 7.401 14685 Z= 0.330 Chirality : 0.046 0.192 1650 Planarity : 0.004 0.039 1917 Dihedral : 5.360 46.204 1569 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.08 % Allowed : 2.36 % 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: -0.53 (0.21), residues: 1323 helix: 1.40 (0.25), residues: 402 sheet: -0.26 (0.32), residues: 258 loop : -1.54 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 127 HIS 0.009 0.001 HIS D 106 PHE 0.012 0.002 PHE C 120 TYR 0.018 0.002 TYR F 83 ARG 0.013 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 190 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.291 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 137 ASN cc_start: 0.9405 (m-40) cc_final: 0.8734 (p0) REVERT: B 54 ARG cc_start: 0.9493 (mtp85) cc_final: 0.8767 (mtp-110) REVERT: B 58 LYS cc_start: 0.9425 (mtmt) cc_final: 0.9096 (mttm) REVERT: B 64 HIS cc_start: 0.9003 (m170) cc_final: 0.8761 (m-70) REVERT: B 86 ASP cc_start: 0.8549 (t0) cc_final: 0.7991 (t0) REVERT: B 90 ASP cc_start: 0.8824 (m-30) cc_final: 0.8599 (m-30) REVERT: B 133 MET cc_start: 0.7751 (ptt) cc_final: 0.7212 (ppp) REVERT: C 70 LEU cc_start: 0.7659 (tp) cc_final: 0.7218 (mt) REVERT: C 98 TYR cc_start: 0.8722 (t80) cc_final: 0.8162 (t80) REVERT: C 100 TYR cc_start: 0.7552 (p90) cc_final: 0.7317 (p90) REVERT: C 137 ASN cc_start: 0.9586 (m-40) cc_final: 0.9133 (p0) REVERT: C 233 TYR cc_start: 0.8352 (m-80) cc_final: 0.7845 (m-80) REVERT: C 261 ARG cc_start: 0.4824 (mtt90) cc_final: 0.3710 (ptt90) REVERT: E 50 LYS cc_start: 0.8682 (mttt) cc_final: 0.8247 (tptm) REVERT: E 71 LEU cc_start: 0.9244 (mt) cc_final: 0.8891 (mt) REVERT: E 98 TYR cc_start: 0.8404 (t80) cc_final: 0.7652 (t80) REVERT: D 54 ARG cc_start: 0.9518 (mtp85) cc_final: 0.8845 (mtp-110) REVERT: D 58 LYS cc_start: 0.9537 (mtmt) cc_final: 0.9087 (mttm) REVERT: D 78 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8837 (mm-40) REVERT: D 86 ASP cc_start: 0.8569 (t0) cc_final: 0.8035 (t0) REVERT: D 90 ASP cc_start: 0.8671 (m-30) cc_final: 0.8397 (m-30) REVERT: D 133 MET cc_start: 0.7575 (ptt) cc_final: 0.7331 (ppp) REVERT: F 59 THR cc_start: 0.9656 (p) cc_final: 0.8991 (p) REVERT: F 63 PHE cc_start: 0.9453 (m-10) cc_final: 0.9156 (m-80) REVERT: F 66 ILE cc_start: 0.9729 (mt) cc_final: 0.9450 (mt) REVERT: F 70 PHE cc_start: 0.8813 (m-80) cc_final: 0.8318 (m-80) REVERT: F 86 ASP cc_start: 0.8439 (t0) cc_final: 0.7874 (t0) REVERT: F 90 ASP cc_start: 0.8945 (m-30) cc_final: 0.8728 (m-30) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.3135 time to fit residues: 78.2450 Evaluate side-chains 135 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 60 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS D 104 ASN F 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10824 Z= 0.180 Angle : 0.565 9.238 14685 Z= 0.298 Chirality : 0.044 0.158 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.723 34.868 1569 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -0.32 (0.22), residues: 1323 helix: 1.59 (0.25), residues: 402 sheet: 0.09 (0.34), residues: 228 loop : -1.47 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 127 HIS 0.007 0.001 HIS F 106 PHE 0.008 0.001 PHE F 70 TYR 0.010 0.001 TYR B 83 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 195 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.232 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: A 98 TYR cc_start: 0.7936 (t80) cc_final: 0.7661 (t80) REVERT: A 137 ASN cc_start: 0.9372 (m-40) cc_final: 0.8687 (p0) REVERT: B 54 ARG cc_start: 0.9485 (mtp85) cc_final: 0.9128 (ptm-80) REVERT: B 64 HIS cc_start: 0.9002 (m170) cc_final: 0.8646 (m90) REVERT: B 66 ILE cc_start: 0.9726 (mt) cc_final: 0.9267 (mt) REVERT: B 70 PHE cc_start: 0.8765 (m-80) cc_final: 0.7291 (m-80) REVERT: B 86 ASP cc_start: 0.8466 (t0) cc_final: 0.7930 (t0) REVERT: B 90 ASP cc_start: 0.8778 (m-30) cc_final: 0.8564 (m-30) REVERT: B 133 MET cc_start: 0.7701 (ptt) cc_final: 0.7194 (ppp) REVERT: C 70 LEU cc_start: 0.7606 (tp) cc_final: 0.7256 (mt) REVERT: C 98 TYR cc_start: 0.8724 (t80) cc_final: 0.8191 (t80) REVERT: C 100 TYR cc_start: 0.7615 (p90) cc_final: 0.7341 (p90) REVERT: C 137 ASN cc_start: 0.9561 (m-40) cc_final: 0.9097 (p0) REVERT: C 233 TYR cc_start: 0.8323 (m-80) cc_final: 0.7885 (m-80) REVERT: C 261 ARG cc_start: 0.4590 (mtt90) cc_final: 0.3312 (ppt90) REVERT: E 50 LYS cc_start: 0.8662 (mttt) cc_final: 0.8225 (tptm) REVERT: E 71 LEU cc_start: 0.9315 (mt) cc_final: 0.8931 (mt) REVERT: E 98 TYR cc_start: 0.8558 (t80) cc_final: 0.7743 (t80) REVERT: E 233 TYR cc_start: 0.8525 (m-80) cc_final: 0.8244 (m-80) REVERT: D 39 LYS cc_start: 0.9725 (mmtm) cc_final: 0.9433 (mmmt) REVERT: D 42 GLN cc_start: 0.9602 (mt0) cc_final: 0.9072 (mt0) REVERT: D 54 ARG cc_start: 0.9491 (mtp85) cc_final: 0.9117 (mtp-110) REVERT: D 59 THR cc_start: 0.9579 (p) cc_final: 0.8915 (p) REVERT: D 63 PHE cc_start: 0.9352 (m-10) cc_final: 0.9035 (m-80) REVERT: D 86 ASP cc_start: 0.8520 (t0) cc_final: 0.8005 (t0) REVERT: D 90 ASP cc_start: 0.8608 (m-30) cc_final: 0.8381 (m-30) REVERT: D 133 MET cc_start: 0.7520 (ptt) cc_final: 0.7272 (ppp) REVERT: F 39 LYS cc_start: 0.9746 (mmtm) cc_final: 0.9529 (mmmt) REVERT: F 59 THR cc_start: 0.9606 (p) cc_final: 0.8861 (p) REVERT: F 62 LYS cc_start: 0.9119 (mptt) cc_final: 0.8823 (mmmm) REVERT: F 63 PHE cc_start: 0.9424 (m-10) cc_final: 0.9070 (m-80) REVERT: F 65 GLN cc_start: 0.9138 (pm20) cc_final: 0.8902 (pm20) REVERT: F 66 ILE cc_start: 0.9712 (mt) cc_final: 0.9154 (mt) REVERT: F 70 PHE cc_start: 0.8721 (m-80) cc_final: 0.8000 (m-80) REVERT: F 86 ASP cc_start: 0.8458 (t0) cc_final: 0.7837 (t0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3053 time to fit residues: 78.1626 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 : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 B 105 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10824 Z= 0.178 Angle : 0.575 10.665 14685 Z= 0.301 Chirality : 0.044 0.162 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.752 44.414 1569 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.22 (0.22), residues: 1323 helix: 1.62 (0.25), residues: 399 sheet: 0.19 (0.34), residues: 234 loop : -1.39 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 127 HIS 0.009 0.001 HIS F 106 PHE 0.033 0.001 PHE B 70 TYR 0.008 0.001 TYR F 83 ARG 0.007 0.000 ARG D 153 *********************** 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 191 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.259 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 98 TYR cc_start: 0.8051 (t80) cc_final: 0.7722 (t80) REVERT: A 137 ASN cc_start: 0.9371 (m-40) cc_final: 0.8729 (p0) REVERT: A 280 GLU cc_start: 0.8966 (mp0) cc_final: 0.8451 (pm20) REVERT: A 288 ILE cc_start: 0.8909 (mt) cc_final: 0.8214 (mt) REVERT: B 54 ARG cc_start: 0.9476 (mtp85) cc_final: 0.9038 (mtp-110) REVERT: B 64 HIS cc_start: 0.8986 (m170) cc_final: 0.8540 (m90) REVERT: B 66 ILE cc_start: 0.9603 (mt) cc_final: 0.9138 (mt) REVERT: B 86 ASP cc_start: 0.8473 (t0) cc_final: 0.7943 (t0) REVERT: B 90 ASP cc_start: 0.8771 (m-30) cc_final: 0.8554 (m-30) REVERT: B 133 MET cc_start: 0.7713 (ptt) cc_final: 0.7188 (ppp) REVERT: C 70 LEU cc_start: 0.7600 (tp) cc_final: 0.7316 (mt) REVERT: C 98 TYR cc_start: 0.8746 (t80) cc_final: 0.8156 (t80) REVERT: C 100 TYR cc_start: 0.7714 (p90) cc_final: 0.7430 (p90) REVERT: C 137 ASN cc_start: 0.9561 (m-40) cc_final: 0.9099 (p0) REVERT: C 184 HIS cc_start: 0.7663 (m90) cc_final: 0.7067 (m-70) REVERT: C 233 TYR cc_start: 0.8313 (m-80) cc_final: 0.7858 (m-80) REVERT: E 50 LYS cc_start: 0.8654 (mttt) cc_final: 0.8205 (tptm) REVERT: E 71 LEU cc_start: 0.9281 (mt) cc_final: 0.8890 (mt) REVERT: E 98 TYR cc_start: 0.8551 (t80) cc_final: 0.7715 (t80) REVERT: E 233 TYR cc_start: 0.8491 (m-80) cc_final: 0.8230 (m-80) REVERT: D 39 LYS cc_start: 0.9725 (mmtm) cc_final: 0.9463 (mmmt) REVERT: D 42 GLN cc_start: 0.9598 (mt0) cc_final: 0.9132 (mt0) REVERT: D 54 ARG cc_start: 0.9459 (mtp85) cc_final: 0.9076 (mtp-110) REVERT: D 59 THR cc_start: 0.9577 (p) cc_final: 0.9182 (p) REVERT: D 63 PHE cc_start: 0.9382 (m-10) cc_final: 0.9094 (m-80) REVERT: D 86 ASP cc_start: 0.8557 (t0) cc_final: 0.8078 (t0) REVERT: D 90 ASP cc_start: 0.8606 (m-30) cc_final: 0.8372 (m-30) REVERT: D 133 MET cc_start: 0.7520 (ptt) cc_final: 0.7275 (ppp) REVERT: F 39 LYS cc_start: 0.9750 (mmtm) cc_final: 0.9548 (mmmt) REVERT: F 59 THR cc_start: 0.9622 (p) cc_final: 0.8940 (p) REVERT: F 62 LYS cc_start: 0.9041 (mptt) cc_final: 0.8766 (mmtp) REVERT: F 63 PHE cc_start: 0.9389 (m-10) cc_final: 0.9011 (m-80) REVERT: F 68 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8754 (mmtt) REVERT: F 86 ASP cc_start: 0.8495 (t0) cc_final: 0.7841 (t0) REVERT: F 90 ASP cc_start: 0.8873 (m-30) cc_final: 0.8660 (m-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2998 time to fit residues: 75.2899 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 : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN E 184 HIS D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5333 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= 0.179 Angle : 0.579 8.820 14685 Z= 0.306 Chirality : 0.044 0.161 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.595 34.279 1569 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.26 (0.22), residues: 1323 helix: 1.51 (0.25), residues: 408 sheet: 0.05 (0.33), residues: 246 loop : -1.38 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 127 HIS 0.009 0.001 HIS F 106 PHE 0.068 0.002 PHE B 70 TYR 0.008 0.001 TYR F 83 ARG 0.005 0.000 ARG B 123 *********************** 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 186 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.160 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: 0.8132 (t80) cc_final: 0.7766 (t80) REVERT: A 137 ASN cc_start: 0.9385 (m-40) cc_final: 0.8722 (p0) REVERT: B 58 LYS cc_start: 0.9426 (mtmt) cc_final: 0.8978 (mtmt) REVERT: B 62 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8876 (mmtt) REVERT: B 64 HIS cc_start: 0.8857 (m170) cc_final: 0.8408 (m90) REVERT: B 86 ASP cc_start: 0.8474 (t0) cc_final: 0.7963 (t0) REVERT: B 133 MET cc_start: 0.7717 (ptt) cc_final: 0.7201 (ppp) REVERT: C 70 LEU cc_start: 0.7576 (tp) cc_final: 0.7320 (mt) REVERT: C 98 TYR cc_start: 0.8743 (t80) cc_final: 0.8174 (t80) REVERT: C 100 TYR cc_start: 0.7737 (p90) cc_final: 0.7463 (p90) REVERT: C 137 ASN cc_start: 0.9557 (m-40) cc_final: 0.9111 (p0) REVERT: C 233 TYR cc_start: 0.8292 (m-80) cc_final: 0.7893 (m-80) REVERT: E 50 LYS cc_start: 0.8658 (mttt) cc_final: 0.8192 (tptm) REVERT: E 71 LEU cc_start: 0.9285 (mt) cc_final: 0.8906 (mt) REVERT: E 98 TYR cc_start: 0.8585 (t80) cc_final: 0.7768 (t80) REVERT: E 233 TYR cc_start: 0.8427 (m-80) cc_final: 0.8203 (m-80) REVERT: D 39 LYS cc_start: 0.9725 (mmtm) cc_final: 0.9465 (mmmt) REVERT: D 42 GLN cc_start: 0.9590 (mt0) cc_final: 0.9133 (mt0) REVERT: D 54 ARG cc_start: 0.9473 (mtp85) cc_final: 0.8890 (mtp-110) REVERT: D 58 LYS cc_start: 0.9365 (mtmt) cc_final: 0.9010 (mttm) REVERT: D 63 PHE cc_start: 0.9359 (m-10) cc_final: 0.9118 (m-80) REVERT: D 64 HIS cc_start: 0.8965 (m170) cc_final: 0.8600 (m-70) REVERT: D 67 GLU cc_start: 0.9374 (pt0) cc_final: 0.8855 (pp20) REVERT: D 86 ASP cc_start: 0.8561 (t0) cc_final: 0.8056 (t0) REVERT: D 90 ASP cc_start: 0.8607 (m-30) cc_final: 0.8369 (m-30) REVERT: D 133 MET cc_start: 0.7537 (ptt) cc_final: 0.7282 (ppp) REVERT: F 39 LYS cc_start: 0.9732 (mmtm) cc_final: 0.9521 (mmmt) REVERT: F 59 THR cc_start: 0.9628 (p) cc_final: 0.9003 (p) REVERT: F 62 LYS cc_start: 0.9065 (mptt) cc_final: 0.8764 (mmtp) REVERT: F 63 PHE cc_start: 0.9369 (m-10) cc_final: 0.9061 (m-80) REVERT: F 66 ILE cc_start: 0.9600 (mt) cc_final: 0.9037 (mt) REVERT: F 70 PHE cc_start: 0.8447 (m-80) cc_final: 0.7963 (m-80) REVERT: F 86 ASP cc_start: 0.8495 (t0) cc_final: 0.7843 (t0) REVERT: F 90 ASP cc_start: 0.8875 (m-30) cc_final: 0.8661 (m-30) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2890 time to fit residues: 71.6104 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 : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 F 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10824 Z= 0.197 Angle : 0.596 12.251 14685 Z= 0.315 Chirality : 0.044 0.165 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.575 34.106 1569 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.25 (0.22), residues: 1323 helix: 1.48 (0.25), residues: 408 sheet: 0.01 (0.32), residues: 246 loop : -1.32 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 127 HIS 0.008 0.001 HIS F 106 PHE 0.040 0.001 PHE B 70 TYR 0.009 0.001 TYR F 83 ARG 0.008 0.000 ARG D 127 *********************** 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 183 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.281 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 98 TYR cc_start: 0.8166 (t80) cc_final: 0.7754 (t80) REVERT: A 137 ASN cc_start: 0.9381 (m-40) cc_final: 0.8726 (p0) REVERT: B 54 ARG cc_start: 0.9476 (mtp85) cc_final: 0.8834 (ptm-80) REVERT: B 58 LYS cc_start: 0.9443 (mtmt) cc_final: 0.9135 (mttm) REVERT: B 62 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8876 (mmmm) REVERT: B 64 HIS cc_start: 0.8858 (m170) cc_final: 0.8389 (m90) REVERT: B 86 ASP cc_start: 0.8513 (t0) cc_final: 0.7944 (t0) REVERT: B 90 ASP cc_start: 0.8825 (m-30) cc_final: 0.8609 (m-30) REVERT: B 133 MET cc_start: 0.7708 (ptt) cc_final: 0.7261 (ppp) REVERT: C 70 LEU cc_start: 0.7606 (tp) cc_final: 0.7314 (mt) REVERT: C 98 TYR cc_start: 0.8739 (t80) cc_final: 0.8163 (t80) REVERT: C 100 TYR cc_start: 0.7603 (p90) cc_final: 0.7373 (p90) REVERT: C 137 ASN cc_start: 0.9569 (m-40) cc_final: 0.9141 (p0) REVERT: C 184 HIS cc_start: 0.7664 (m90) cc_final: 0.7096 (m-70) REVERT: C 233 TYR cc_start: 0.8285 (m-80) cc_final: 0.7860 (m-80) REVERT: E 71 LEU cc_start: 0.9273 (mt) cc_final: 0.8878 (mt) REVERT: E 98 TYR cc_start: 0.8610 (t80) cc_final: 0.7785 (t80) REVERT: E 233 TYR cc_start: 0.8442 (m-80) cc_final: 0.8202 (m-80) REVERT: D 54 ARG cc_start: 0.9479 (mtp85) cc_final: 0.9088 (mtp-110) REVERT: D 59 THR cc_start: 0.9463 (p) cc_final: 0.8862 (p) REVERT: D 63 PHE cc_start: 0.9374 (m-10) cc_final: 0.9066 (m-80) REVERT: D 64 HIS cc_start: 0.8999 (m170) cc_final: 0.8654 (m-70) REVERT: D 69 GLU cc_start: 0.8975 (mp0) cc_final: 0.8754 (mp0) REVERT: D 86 ASP cc_start: 0.8567 (t0) cc_final: 0.8065 (t0) REVERT: D 90 ASP cc_start: 0.8632 (m-30) cc_final: 0.8391 (m-30) REVERT: D 133 MET cc_start: 0.7561 (ptt) cc_final: 0.7226 (ppp) REVERT: F 59 THR cc_start: 0.9622 (p) cc_final: 0.8835 (p) REVERT: F 63 PHE cc_start: 0.9360 (m-10) cc_final: 0.9024 (m-80) REVERT: F 68 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8657 (mmtt) REVERT: F 86 ASP cc_start: 0.8494 (t0) cc_final: 0.7840 (t0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2879 time to fit residues: 70.0638 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 : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 131 optimal weight: 0.0470 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN E 184 HIS D 104 ASN F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10824 Z= 0.167 Angle : 0.594 11.431 14685 Z= 0.314 Chirality : 0.045 0.167 1650 Planarity : 0.004 0.042 1917 Dihedral : 4.361 34.099 1569 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.05 (0.22), residues: 1323 helix: 1.65 (0.25), residues: 405 sheet: 0.13 (0.33), residues: 246 loop : -1.19 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 127 HIS 0.008 0.001 HIS F 106 PHE 0.031 0.001 PHE B 70 TYR 0.007 0.001 TYR E 98 ARG 0.008 0.000 ARG D 127 ********************** 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 182 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.284 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: 0.8178 (t80) cc_final: 0.7747 (t80) REVERT: A 137 ASN cc_start: 0.9378 (m-40) cc_final: 0.8733 (p0) REVERT: A 280 GLU cc_start: 0.9051 (mp0) cc_final: 0.8695 (mp0) REVERT: B 54 ARG cc_start: 0.9473 (mtp85) cc_final: 0.8839 (ptm-80) REVERT: B 58 LYS cc_start: 0.9448 (mtmt) cc_final: 0.9152 (mttm) REVERT: B 62 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8768 (mmmm) REVERT: B 64 HIS cc_start: 0.8774 (m170) cc_final: 0.8295 (m90) REVERT: B 65 GLN cc_start: 0.9010 (pm20) cc_final: 0.8753 (pm20) REVERT: B 78 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8476 (mm110) REVERT: B 86 ASP cc_start: 0.8500 (t0) cc_final: 0.7925 (t0) REVERT: B 90 ASP cc_start: 0.8839 (m-30) cc_final: 0.8624 (m-30) REVERT: B 123 ARG cc_start: 0.9116 (pmt-80) cc_final: 0.8906 (pmt-80) REVERT: B 133 MET cc_start: 0.7624 (ptt) cc_final: 0.7202 (ppp) REVERT: C 70 LEU cc_start: 0.7576 (tp) cc_final: 0.7305 (mt) REVERT: C 98 TYR cc_start: 0.8739 (t80) cc_final: 0.8152 (t80) REVERT: C 100 TYR cc_start: 0.7585 (p90) cc_final: 0.7334 (p90) REVERT: C 137 ASN cc_start: 0.9560 (m-40) cc_final: 0.9119 (p0) REVERT: C 233 TYR cc_start: 0.8289 (m-80) cc_final: 0.7908 (m-80) REVERT: E 50 LYS cc_start: 0.8648 (mttt) cc_final: 0.8153 (tttp) REVERT: E 71 LEU cc_start: 0.9287 (mt) cc_final: 0.8944 (mt) REVERT: E 98 TYR cc_start: 0.8571 (t80) cc_final: 0.7755 (t80) REVERT: E 233 TYR cc_start: 0.8423 (m-80) cc_final: 0.8168 (m-80) REVERT: D 39 LYS cc_start: 0.9735 (mmtm) cc_final: 0.9509 (mmmt) REVERT: D 42 GLN cc_start: 0.9591 (mt0) cc_final: 0.9122 (mt0) REVERT: D 54 ARG cc_start: 0.9480 (mtp85) cc_final: 0.9165 (mtp-110) REVERT: D 64 HIS cc_start: 0.8965 (m170) cc_final: 0.8597 (m-70) REVERT: D 69 GLU cc_start: 0.8928 (mp0) cc_final: 0.8699 (mp0) REVERT: D 86 ASP cc_start: 0.8557 (t0) cc_final: 0.8038 (t0) REVERT: D 90 ASP cc_start: 0.8604 (m-30) cc_final: 0.8365 (m-30) REVERT: D 115 MET cc_start: 0.8823 (tpt) cc_final: 0.8602 (tpt) REVERT: D 133 MET cc_start: 0.7641 (ptt) cc_final: 0.7279 (ppp) REVERT: F 39 LYS cc_start: 0.9744 (mmtm) cc_final: 0.9535 (mmmt) REVERT: F 59 THR cc_start: 0.9617 (p) cc_final: 0.8790 (p) REVERT: F 63 PHE cc_start: 0.9356 (m-10) cc_final: 0.9028 (m-80) REVERT: F 64 HIS cc_start: 0.8835 (m170) cc_final: 0.8470 (m90) REVERT: F 86 ASP cc_start: 0.8456 (t0) cc_final: 0.7797 (t0) REVERT: F 90 ASP cc_start: 0.8858 (m-30) cc_final: 0.8632 (m-30) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2836 time to fit residues: 68.9732 Evaluate side-chains 143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 104 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- 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 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.086751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.060587 restraints weight = 51859.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058620 restraints weight = 28760.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.059065 restraints weight = 25911.209| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10824 Z= 0.256 Angle : 0.618 9.766 14685 Z= 0.329 Chirality : 0.045 0.177 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.755 33.933 1569 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.28 (0.22), residues: 1323 helix: 1.49 (0.25), residues: 408 sheet: -0.11 (0.32), residues: 252 loop : -1.32 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 127 HIS 0.009 0.001 HIS F 106 PHE 0.010 0.001 PHE F 70 TYR 0.013 0.002 TYR F 83 ARG 0.007 0.001 ARG D 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2525.68 seconds wall clock time: 47 minutes 9.93 seconds (2829.93 seconds total)