Starting phenix.real_space_refine on Wed Sep 25 10:17:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/09_2024/7yqd_34024.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/09_2024/7yqd_34024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/09_2024/7yqd_34024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/09_2024/7yqd_34024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/09_2024/7yqd_34024.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/09_2024/7yqd_34024.cif" } resolution = 3.4 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= 0.000 sd= 0.022 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 28 5.16 5 C 6671 2.51 5 N 1771 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.56, per 1000 atoms: 0.35 Number of scatterers: 10290 At special positions: 0 Unit cell: (110.24, 112.32, 78, 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 28 16.00 O 1820 8.00 N 1771 7.00 C 6671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE A 52 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 143 Proline residue: A 124 - end of helix removed outlier: 3.598A pdb=" N THR A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 244 removed outlier: 4.113A pdb=" N ARG A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE B 52 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 Proline residue: B 124 - end of helix removed outlier: 3.598A pdb=" N THR B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 32 through 47 Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE C 52 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 143 Proline residue: C 124 - end of helix removed outlier: 3.598A pdb=" N THR C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 207 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 48 through 52 removed outlier: 4.075A pdb=" N ILE D 52 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 143 Proline residue: D 124 - end of helix removed outlier: 3.598A pdb=" N THR D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 32 Processing helix chain 'E' and resid 32 through 47 Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE E 52 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 143 Proline residue: E 124 - end of helix removed outlier: 3.598A pdb=" N THR E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 244 removed outlier: 4.113A pdb=" N ARG E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 207 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 32 Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE F 52 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 143 Proline residue: F 124 - end of helix removed outlier: 3.598A pdb=" N THR F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA F 194 " --> pdb=" O VAL F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 207 " --> pdb=" O ARG F 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS F 241 " --> pdb=" O LYS F 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 32 Processing helix chain 'G' and resid 32 through 47 Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE G 52 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 143 Proline residue: G 124 - end of helix removed outlier: 3.599A pdb=" N THR G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 196 removed outlier: 3.543A pdb=" N TYR G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 207 " --> pdb=" O ARG G 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS G 241 " --> pdb=" O LYS G 237 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2772 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: 2.64 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1938 1.33 - 1.45: 2164 1.45 - 1.57: 6272 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 10423 Sorted by residual: bond pdb=" N ILE F 144 " pdb=" CA ILE F 144 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N ILE C 144 " pdb=" CA ILE C 144 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N ILE B 144 " pdb=" CA ILE B 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.29e+01 bond pdb=" N ILE D 144 " pdb=" CA ILE D 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.28e+01 bond pdb=" N ILE E 144 " pdb=" CA ILE E 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.28e+01 ... (remaining 10418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 8209 1.13 - 2.27: 3856 2.27 - 3.40: 1853 3.40 - 4.54: 168 4.54 - 5.67: 33 Bond angle restraints: 14119 Sorted by residual: angle pdb=" CA ILE D 144 " pdb=" C ILE D 144 " pdb=" N PRO D 145 " ideal model delta sigma weight residual 119.30 122.49 -3.19 8.10e-01 1.52e+00 1.55e+01 angle pdb=" CA ILE G 144 " pdb=" C ILE G 144 " pdb=" N PRO G 145 " ideal model delta sigma weight residual 119.30 122.48 -3.18 8.10e-01 1.52e+00 1.54e+01 angle pdb=" CA ILE A 144 " pdb=" C ILE A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 119.30 122.47 -3.17 8.10e-01 1.52e+00 1.53e+01 angle pdb=" CA ILE E 144 " pdb=" C ILE E 144 " pdb=" N PRO E 145 " ideal model delta sigma weight residual 119.30 122.46 -3.16 8.10e-01 1.52e+00 1.52e+01 angle pdb=" CA ILE F 144 " pdb=" C ILE F 144 " pdb=" N PRO F 145 " ideal model delta sigma weight residual 119.30 122.45 -3.15 8.10e-01 1.52e+00 1.52e+01 ... (remaining 14114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.67: 5559 11.67 - 23.35: 566 23.35 - 35.02: 189 35.02 - 46.69: 105 46.69 - 58.36: 49 Dihedral angle restraints: 6468 sinusoidal: 2464 harmonic: 4004 Sorted by residual: dihedral pdb=" C GLN A 178 " pdb=" N GLN A 178 " pdb=" CA GLN A 178 " pdb=" CB GLN A 178 " ideal model delta harmonic sigma weight residual -122.60 -133.35 10.75 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C GLN E 178 " pdb=" N GLN E 178 " pdb=" CA GLN E 178 " pdb=" CB GLN E 178 " ideal model delta harmonic sigma weight residual -122.60 -133.32 10.72 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C GLN B 178 " pdb=" N GLN B 178 " pdb=" CA GLN B 178 " pdb=" CB GLN B 178 " ideal model delta harmonic sigma weight residual -122.60 -133.31 10.71 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 684 0.067 - 0.134: 761 0.134 - 0.201: 277 0.201 - 0.268: 49 0.268 - 0.335: 7 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CA GLN A 178 " pdb=" N GLN A 178 " pdb=" C GLN A 178 " pdb=" CB GLN A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA GLN D 178 " pdb=" N GLN D 178 " pdb=" C GLN D 178 " pdb=" CB GLN D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA GLN E 178 " pdb=" N GLN E 178 " pdb=" C GLN E 178 " pdb=" CB GLN E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1775 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 120 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C GLU A 120 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU A 120 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 121 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 120 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLU G 120 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU G 120 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS G 121 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 120 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C GLU C 120 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU C 120 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS C 121 " 0.008 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3223 2.85 - 3.36: 11277 3.36 - 3.87: 15518 3.87 - 4.39: 18213 4.39 - 4.90: 30412 Nonbonded interactions: 78643 Sorted by model distance: nonbonded pdb=" CB ASN F 226 " pdb=" CE MET G 138 " model vdw 2.335 3.860 nonbonded pdb=" CB ASN A 226 " pdb=" CE MET C 138 " model vdw 2.343 3.860 nonbonded pdb=" CB ASN C 226 " pdb=" CE MET D 138 " model vdw 2.349 3.860 nonbonded pdb=" CB ASN D 226 " pdb=" CE MET E 138 " model vdw 2.349 3.860 nonbonded pdb=" CE MET B 138 " pdb=" CB ASN G 226 " model vdw 2.352 3.860 ... (remaining 78638 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 20.940 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.012 0.038 10423 Z= 0.762 Angle : 1.460 5.669 14119 Z= 1.214 Chirality : 0.104 0.335 1778 Planarity : 0.005 0.022 1722 Dihedral : 13.548 58.363 3822 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 7.63 % Allowed : 7.92 % Favored : 84.45 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.20 (0.18), residues: 1288 helix: 4.77 (0.11), residues: 1092 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 139 HIS 0.003 0.001 HIS E 232 PHE 0.006 0.001 PHE G 44 TYR 0.010 0.002 TYR G 183 ARG 0.002 0.001 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 372 time to evaluate : 1.438 Fit side-chains REVERT: A 54 ASP cc_start: 0.8387 (t0) cc_final: 0.7993 (t70) REVERT: A 238 ASN cc_start: 0.8511 (m-40) cc_final: 0.8253 (m-40) REVERT: B 37 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9240 (mmtt) REVERT: B 54 ASP cc_start: 0.8484 (t0) cc_final: 0.7906 (t0) REVERT: B 201 ASP cc_start: 0.7901 (m-30) cc_final: 0.7485 (m-30) REVERT: C 54 ASP cc_start: 0.8467 (t0) cc_final: 0.8071 (t0) REVERT: C 234 MET cc_start: 0.9020 (ttm) cc_final: 0.8798 (ttm) REVERT: D 37 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9150 (mmtt) REVERT: D 54 ASP cc_start: 0.8526 (t0) cc_final: 0.7974 (t0) REVERT: D 166 ARG cc_start: 0.8996 (ttp-170) cc_final: 0.8636 (mtt90) REVERT: E 54 ASP cc_start: 0.8478 (t0) cc_final: 0.8030 (t70) REVERT: F 54 ASP cc_start: 0.8476 (t0) cc_final: 0.8201 (t0) REVERT: G 54 ASP cc_start: 0.8449 (t0) cc_final: 0.8092 (t0) REVERT: G 117 ASP cc_start: 0.8424 (m-30) cc_final: 0.8016 (m-30) outliers start: 81 outliers final: 40 residues processed: 425 average time/residue: 0.2412 time to fit residues: 138.0696 Evaluate side-chains 359 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 317 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 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 9 GLN A 112 ASN A 158 GLN A 178 GLN B 112 ASN B 178 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN E 112 ASN E 178 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN G 178 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10423 Z= 0.211 Angle : 0.540 8.802 14119 Z= 0.297 Chirality : 0.036 0.133 1778 Planarity : 0.004 0.043 1722 Dihedral : 8.186 58.968 1498 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.84 % Allowed : 15.27 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.48 (0.19), residues: 1288 helix: 4.19 (0.12), residues: 1092 sheet: None (None), residues: 0 loop : -0.36 (0.28), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 139 HIS 0.003 0.001 HIS F 59 PHE 0.006 0.001 PHE A 18 TYR 0.017 0.001 TYR F 214 ARG 0.004 0.001 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 334 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8369 (t0) cc_final: 0.7980 (t70) REVERT: A 57 GLN cc_start: 0.8192 (mp10) cc_final: 0.7947 (mp10) REVERT: B 37 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9063 (mmtt) REVERT: B 54 ASP cc_start: 0.8450 (t0) cc_final: 0.7952 (t70) REVERT: B 128 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8256 (mm) REVERT: B 166 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8364 (ttp-170) REVERT: C 54 ASP cc_start: 0.8342 (t0) cc_final: 0.7877 (t0) REVERT: C 166 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8472 (ttp-170) REVERT: C 234 MET cc_start: 0.9013 (ttm) cc_final: 0.8738 (tmm) REVERT: D 37 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8932 (mmtt) REVERT: D 54 ASP cc_start: 0.8503 (t0) cc_final: 0.8183 (t0) REVERT: D 166 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8579 (mtt90) REVERT: E 54 ASP cc_start: 0.8366 (t0) cc_final: 0.7891 (t0) REVERT: F 54 ASP cc_start: 0.8394 (t0) cc_final: 0.8086 (t0) REVERT: F 166 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8550 (ttp-170) REVERT: F 210 ASP cc_start: 0.7974 (m-30) cc_final: 0.7562 (m-30) REVERT: G 54 ASP cc_start: 0.8405 (t0) cc_final: 0.7900 (t0) outliers start: 62 outliers final: 32 residues processed: 368 average time/residue: 0.2261 time to fit residues: 113.6379 Evaluate side-chains 339 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 300 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 0.0070 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 178 GLN A 238 ASN B 178 GLN B 238 ASN C 112 ASN C 178 GLN D 178 GLN E 112 ASN E 178 GLN F 178 GLN F 238 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10423 Z= 0.188 Angle : 0.482 6.643 14119 Z= 0.265 Chirality : 0.035 0.139 1778 Planarity : 0.004 0.029 1722 Dihedral : 6.102 57.421 1464 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.28 % Allowed : 18.28 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.18 (0.20), residues: 1288 helix: 3.96 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.30 (0.30), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 139 HIS 0.002 0.000 HIS F 59 PHE 0.004 0.001 PHE E 18 TYR 0.012 0.001 TYR F 214 ARG 0.007 0.001 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 317 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8413 (t0) cc_final: 0.7974 (t70) REVERT: B 54 ASP cc_start: 0.8381 (t0) cc_final: 0.7728 (t70) REVERT: B 166 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8436 (ttp-170) REVERT: B 210 ASP cc_start: 0.8424 (m-30) cc_final: 0.8068 (m-30) REVERT: C 54 ASP cc_start: 0.8371 (t0) cc_final: 0.7928 (t0) REVERT: C 117 ASP cc_start: 0.8199 (m-30) cc_final: 0.7991 (m-30) REVERT: C 142 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 166 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8621 (ttp-170) REVERT: D 37 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8690 (mmmt) REVERT: D 54 ASP cc_start: 0.8462 (t0) cc_final: 0.7946 (t0) REVERT: D 57 GLN cc_start: 0.8195 (mp10) cc_final: 0.7953 (mp10) REVERT: D 166 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8626 (mtt90) REVERT: D 188 LYS cc_start: 0.8617 (tttt) cc_final: 0.8366 (ttmm) REVERT: D 208 GLU cc_start: 0.8357 (tp30) cc_final: 0.8044 (tp30) REVERT: E 54 ASP cc_start: 0.8277 (t0) cc_final: 0.7979 (t0) REVERT: E 138 MET cc_start: 0.8300 (tpp) cc_final: 0.8024 (tpp) REVERT: E 158 GLN cc_start: 0.8365 (tt0) cc_final: 0.8155 (tt0) REVERT: F 54 ASP cc_start: 0.8305 (t0) cc_final: 0.7966 (t0) REVERT: F 210 ASP cc_start: 0.7813 (m-30) cc_final: 0.7478 (m-30) REVERT: G 54 ASP cc_start: 0.8309 (t0) cc_final: 0.7813 (t0) outliers start: 56 outliers final: 37 residues processed: 352 average time/residue: 0.2382 time to fit residues: 114.4956 Evaluate side-chains 339 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 297 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 238 ASN B 9 GLN B 112 ASN B 238 ASN C 112 ASN E 112 ASN E 178 GLN E 238 ASN F 226 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10423 Z= 0.193 Angle : 0.478 6.038 14119 Z= 0.261 Chirality : 0.035 0.123 1778 Planarity : 0.003 0.027 1722 Dihedral : 5.753 56.097 1458 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.15 % Allowed : 20.17 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.97 (0.20), residues: 1288 helix: 3.80 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.27 (0.30), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 139 HIS 0.002 0.000 HIS D 59 PHE 0.005 0.001 PHE E 18 TYR 0.007 0.001 TYR F 214 ARG 0.008 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8398 (t0) cc_final: 0.7903 (t0) REVERT: B 54 ASP cc_start: 0.8309 (t0) cc_final: 0.7731 (t70) REVERT: B 57 GLN cc_start: 0.8208 (mp10) cc_final: 0.7939 (mp10) REVERT: B 166 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8454 (ttp-170) REVERT: B 210 ASP cc_start: 0.8443 (m-30) cc_final: 0.8097 (m-30) REVERT: C 54 ASP cc_start: 0.8500 (t0) cc_final: 0.8146 (t70) REVERT: D 37 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8775 (mmmt) REVERT: D 54 ASP cc_start: 0.8477 (t0) cc_final: 0.8119 (t0) REVERT: D 188 LYS cc_start: 0.8595 (tttt) cc_final: 0.8292 (ttmm) REVERT: D 208 GLU cc_start: 0.8386 (tp30) cc_final: 0.8060 (tp30) REVERT: E 54 ASP cc_start: 0.8290 (t0) cc_final: 0.7860 (t0) REVERT: F 54 ASP cc_start: 0.8324 (t0) cc_final: 0.8092 (t0) REVERT: F 109 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6319 (mp) REVERT: F 166 ARG cc_start: 0.8568 (ttp-170) cc_final: 0.8204 (mtt90) REVERT: F 210 ASP cc_start: 0.7860 (m-30) cc_final: 0.7612 (m-30) REVERT: G 54 ASP cc_start: 0.8317 (t0) cc_final: 0.7952 (t0) outliers start: 44 outliers final: 29 residues processed: 332 average time/residue: 0.2264 time to fit residues: 103.3756 Evaluate side-chains 320 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 114 GLN B 178 GLN C 112 ASN C 178 GLN D 178 GLN F 178 GLN G 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10423 Z= 0.195 Angle : 0.492 7.171 14119 Z= 0.267 Chirality : 0.036 0.124 1778 Planarity : 0.004 0.033 1722 Dihedral : 5.736 55.751 1458 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 4.34 % Allowed : 19.60 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.21), residues: 1288 helix: 3.73 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 139 HIS 0.001 0.000 HIS D 59 PHE 0.005 0.001 PHE E 18 TYR 0.005 0.001 TYR G 183 ARG 0.011 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 292 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8471 (t0) cc_final: 0.8020 (t0) REVERT: B 54 ASP cc_start: 0.8376 (t0) cc_final: 0.7858 (t70) REVERT: B 210 ASP cc_start: 0.8319 (m-30) cc_final: 0.8002 (m-30) REVERT: C 54 ASP cc_start: 0.8442 (t0) cc_final: 0.8003 (t70) REVERT: C 142 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 37 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8735 (mmmt) REVERT: D 54 ASP cc_start: 0.8439 (t0) cc_final: 0.7959 (t0) REVERT: D 57 GLN cc_start: 0.8215 (mp10) cc_final: 0.7960 (mp10) REVERT: D 142 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 188 LYS cc_start: 0.8592 (tttt) cc_final: 0.8274 (ttmm) REVERT: D 208 GLU cc_start: 0.8396 (tp30) cc_final: 0.8051 (tp30) REVERT: E 54 ASP cc_start: 0.8184 (t0) cc_final: 0.7969 (t0) REVERT: F 54 ASP cc_start: 0.8332 (t0) cc_final: 0.7882 (t0) REVERT: F 109 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6171 (mp) REVERT: F 166 ARG cc_start: 0.8561 (ttp-170) cc_final: 0.8018 (mtm-85) REVERT: G 54 ASP cc_start: 0.8326 (t0) cc_final: 0.7798 (t0) outliers start: 46 outliers final: 36 residues processed: 324 average time/residue: 0.2404 time to fit residues: 107.8681 Evaluate side-chains 321 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 281 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.0170 chunk 67 optimal weight: 0.9980 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN A 238 ASN B 178 GLN B 226 ASN B 238 ASN C 112 ASN C 178 GLN C 226 ASN D 226 ASN E 112 ASN E 238 ASN F 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10423 Z= 0.187 Angle : 0.495 6.317 14119 Z= 0.270 Chirality : 0.035 0.127 1778 Planarity : 0.004 0.039 1722 Dihedral : 5.595 55.617 1456 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 4.24 % Allowed : 19.98 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.21), residues: 1288 helix: 3.70 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 139 HIS 0.001 0.000 HIS D 59 PHE 0.005 0.001 PHE E 18 TYR 0.004 0.001 TYR A 183 ARG 0.013 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 291 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8532 (t0) cc_final: 0.7527 (t0) REVERT: A 57 GLN cc_start: 0.8170 (mp10) cc_final: 0.7674 (mp10) REVERT: A 112 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8062 (t0) REVERT: B 54 ASP cc_start: 0.8262 (t0) cc_final: 0.7857 (t70) REVERT: B 210 ASP cc_start: 0.8345 (m-30) cc_final: 0.8054 (m-30) REVERT: C 54 ASP cc_start: 0.8431 (t0) cc_final: 0.7956 (t0) REVERT: C 142 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8556 (mp) REVERT: D 37 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8737 (mmmt) REVERT: D 54 ASP cc_start: 0.8434 (t0) cc_final: 0.8074 (t0) REVERT: D 142 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8515 (mp) REVERT: D 188 LYS cc_start: 0.8577 (tttt) cc_final: 0.8260 (ttmm) REVERT: D 203 ARG cc_start: 0.7019 (mtp85) cc_final: 0.6800 (mtp85) REVERT: D 208 GLU cc_start: 0.8414 (tp30) cc_final: 0.8059 (tp30) REVERT: E 54 ASP cc_start: 0.8314 (t0) cc_final: 0.7932 (t0) REVERT: F 54 ASP cc_start: 0.8235 (t0) cc_final: 0.7996 (t0) REVERT: F 109 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6124 (mp) REVERT: F 210 ASP cc_start: 0.7783 (m-30) cc_final: 0.7500 (m-30) REVERT: F 226 ASN cc_start: 0.8263 (m-40) cc_final: 0.8016 (m110) REVERT: G 54 ASP cc_start: 0.8343 (t0) cc_final: 0.7637 (t0) REVERT: G 57 GLN cc_start: 0.8290 (mp10) cc_final: 0.8035 (mp10) outliers start: 45 outliers final: 33 residues processed: 327 average time/residue: 0.2248 time to fit residues: 102.0977 Evaluate side-chains 315 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 277 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.0670 chunk 14 optimal weight: 0.0570 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.0470 chunk 80 optimal weight: 0.0870 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 238 ASN C 112 ASN C 178 GLN D 178 GLN E 112 ASN F 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10423 Z= 0.161 Angle : 0.493 6.058 14119 Z= 0.268 Chirality : 0.035 0.144 1778 Planarity : 0.004 0.044 1722 Dihedral : 5.319 57.090 1452 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.11 % Allowed : 20.92 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.90 (0.21), residues: 1288 helix: 3.73 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.07 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 139 HIS 0.001 0.000 HIS E 59 PHE 0.005 0.001 PHE E 18 TYR 0.007 0.001 TYR B 214 ARG 0.015 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 308 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8463 (t0) cc_final: 0.7682 (t0) REVERT: A 57 GLN cc_start: 0.8134 (mp10) cc_final: 0.7815 (mp10) REVERT: A 112 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8185 (t0) REVERT: B 54 ASP cc_start: 0.8281 (t0) cc_final: 0.7854 (t70) REVERT: B 210 ASP cc_start: 0.8254 (m-30) cc_final: 0.7999 (m-30) REVERT: C 54 ASP cc_start: 0.8369 (t0) cc_final: 0.7659 (t0) REVERT: D 37 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8648 (mmmt) REVERT: D 54 ASP cc_start: 0.8393 (t0) cc_final: 0.7747 (t0) REVERT: D 57 GLN cc_start: 0.8225 (mp10) cc_final: 0.7999 (mp10) REVERT: E 54 ASP cc_start: 0.8221 (t0) cc_final: 0.7944 (t0) REVERT: F 54 ASP cc_start: 0.8169 (t0) cc_final: 0.7904 (t70) REVERT: G 54 ASP cc_start: 0.8364 (t0) cc_final: 0.7672 (t0) REVERT: G 191 SER cc_start: 0.9249 (t) cc_final: 0.8933 (p) outliers start: 33 outliers final: 25 residues processed: 334 average time/residue: 0.2028 time to fit residues: 96.2117 Evaluate side-chains 311 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 284 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN B 112 ASN C 112 ASN D 226 ASN E 226 ASN E 238 ASN F 112 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10423 Z= 0.316 Angle : 0.614 14.676 14119 Z= 0.322 Chirality : 0.039 0.158 1778 Planarity : 0.004 0.055 1722 Dihedral : 5.366 53.599 1446 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 3.30 % Allowed : 21.58 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.21), residues: 1288 helix: 3.46 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.68 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 139 HIS 0.003 0.001 HIS D 59 PHE 0.009 0.001 PHE C 33 TYR 0.009 0.001 TYR E 214 ARG 0.014 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8559 (t0) cc_final: 0.7867 (t0) REVERT: A 138 MET cc_start: 0.8996 (tpp) cc_final: 0.8345 (tpt) REVERT: B 54 ASP cc_start: 0.8372 (t0) cc_final: 0.7643 (t70) REVERT: B 57 GLN cc_start: 0.8272 (mp10) cc_final: 0.7798 (mp10) REVERT: C 238 ASN cc_start: 0.8810 (m-40) cc_final: 0.8606 (m-40) REVERT: D 37 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8739 (mmmt) REVERT: D 54 ASP cc_start: 0.8511 (t0) cc_final: 0.8093 (t0) REVERT: D 188 LYS cc_start: 0.8602 (tttt) cc_final: 0.8317 (ttmm) REVERT: D 203 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7208 (mtp85) REVERT: E 54 ASP cc_start: 0.8404 (t0) cc_final: 0.8134 (t0) REVERT: F 226 ASN cc_start: 0.9033 (m-40) cc_final: 0.8681 (m-40) REVERT: G 54 ASP cc_start: 0.8352 (t0) cc_final: 0.7921 (t0) outliers start: 35 outliers final: 25 residues processed: 309 average time/residue: 0.2308 time to fit residues: 97.7071 Evaluate side-chains 301 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 275 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 114 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN B 112 ASN B 178 GLN B 238 ASN C 112 ASN C 178 GLN D 178 GLN E 112 ASN F 178 GLN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10423 Z= 0.194 Angle : 0.559 14.231 14119 Z= 0.298 Chirality : 0.036 0.181 1778 Planarity : 0.004 0.055 1722 Dihedral : 5.175 54.436 1444 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.11 % Allowed : 22.15 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.21), residues: 1288 helix: 3.59 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.61 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 139 HIS 0.001 0.000 HIS A 53 PHE 0.005 0.001 PHE E 18 TYR 0.007 0.001 TYR D 214 ARG 0.016 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8417 (t0) cc_final: 0.7827 (t0) REVERT: A 57 GLN cc_start: 0.8110 (mp10) cc_final: 0.7811 (mp10) REVERT: A 138 MET cc_start: 0.9087 (tpp) cc_final: 0.8294 (tpt) REVERT: B 54 ASP cc_start: 0.8389 (t0) cc_final: 0.7671 (t70) REVERT: B 57 GLN cc_start: 0.8257 (mp10) cc_final: 0.7807 (mp10) REVERT: C 54 ASP cc_start: 0.8637 (t70) cc_final: 0.8261 (t0) REVERT: C 192 LYS cc_start: 0.9204 (mmtm) cc_final: 0.9000 (mmtt) REVERT: D 37 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8762 (mmmt) REVERT: D 188 LYS cc_start: 0.8460 (tttt) cc_final: 0.8173 (ttmm) outliers start: 33 outliers final: 25 residues processed: 302 average time/residue: 0.2234 time to fit residues: 93.1290 Evaluate side-chains 299 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 273 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN B 112 ASN B 178 GLN B 238 ASN E 112 ASN F 178 GLN G 112 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10423 Z= 0.223 Angle : 0.567 11.619 14119 Z= 0.305 Chirality : 0.037 0.176 1778 Planarity : 0.004 0.052 1722 Dihedral : 5.002 54.085 1440 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.73 % Allowed : 22.05 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.51 (0.21), residues: 1288 helix: 3.53 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.73 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 139 HIS 0.002 0.000 HIS G 53 PHE 0.006 0.001 PHE B 18 TYR 0.005 0.001 TYR C 228 ARG 0.015 0.001 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 273 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8416 (t0) cc_final: 0.7685 (t0) REVERT: A 57 GLN cc_start: 0.8138 (mp10) cc_final: 0.7810 (mp10) REVERT: B 54 ASP cc_start: 0.8420 (t0) cc_final: 0.7657 (t70) REVERT: B 57 GLN cc_start: 0.8287 (mp10) cc_final: 0.7815 (mp10) REVERT: B 208 GLU cc_start: 0.8271 (tp30) cc_final: 0.8064 (tp30) REVERT: C 54 ASP cc_start: 0.8674 (t70) cc_final: 0.8214 (t0) REVERT: D 37 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8776 (mmmt) REVERT: D 54 ASP cc_start: 0.8069 (t0) cc_final: 0.7660 (t0) REVERT: D 188 LYS cc_start: 0.8545 (tttt) cc_final: 0.8239 (ttmm) REVERT: F 188 LYS cc_start: 0.8677 (tttp) cc_final: 0.8423 (ttmm) outliers start: 29 outliers final: 25 residues processed: 299 average time/residue: 0.2354 time to fit residues: 96.4782 Evaluate side-chains 298 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN B 112 ASN B 178 GLN D 178 GLN E 112 ASN ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN G 57 GLN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.091256 restraints weight = 18281.626| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.71 r_work: 0.3002 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10423 Z= 0.198 Angle : 0.572 14.333 14119 Z= 0.303 Chirality : 0.037 0.199 1778 Planarity : 0.004 0.050 1722 Dihedral : 4.968 54.452 1440 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.02 % Allowed : 22.15 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.46 (0.21), residues: 1288 helix: 3.50 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.77 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 139 HIS 0.002 0.000 HIS G 53 PHE 0.006 0.001 PHE E 18 TYR 0.006 0.001 TYR D 214 ARG 0.015 0.001 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.57 seconds wall clock time: 45 minutes 21.98 seconds (2721.98 seconds total)