Starting phenix.real_space_refine on Sun Dec 29 12:45:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqg_33395/12_2024/7xqg_33395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqg_33395/12_2024/7xqg_33395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqg_33395/12_2024/7xqg_33395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqg_33395/12_2024/7xqg_33395.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqg_33395/12_2024/7xqg_33395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqg_33395/12_2024/7xqg_33395.cif" } resolution = 3.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 48 5.16 5 C 6846 2.51 5 N 1566 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10206 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 4.50, per 1000 atoms: 0.44 Number of scatterers: 10206 At special positions: 0 Unit cell: (106, 111.088, 99.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 6 15.00 O 1740 8.00 N 1566 7.00 C 6846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " 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 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.797A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 110 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 151 through 177 Processing helix chain 'A' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 110 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 151 through 177 Processing helix chain 'B' and resid 202 through 237 removed outlier: 3.583A pdb=" N LYS B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.797A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 110 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 151 through 177 Processing helix chain 'C' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.602A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 110 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 151 through 177 Processing helix chain 'D' and resid 202 through 237 removed outlier: 3.583A pdb=" N LYS D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 removed outlier: 3.512A pdb=" N GLN E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.534A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.795A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 110 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 151 through 177 Processing helix chain 'E' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 removed outlier: 3.511A pdb=" N GLN F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 40 removed outlier: 3.535A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.603A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.796A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 110 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 151 through 177 Processing helix chain 'F' and resid 202 through 237 removed outlier: 3.584A pdb=" N LYS F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2088 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: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1597 1.33 - 1.45: 2897 1.45 - 1.57: 5910 1.57 - 1.69: 12 1.69 - 1.81: 60 Bond restraints: 10476 Sorted by residual: bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.95e-01 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.90e-01 bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.82e-01 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 13864 1.22 - 2.44: 244 2.44 - 3.66: 52 3.66 - 4.88: 12 4.88 - 6.10: 18 Bond angle restraints: 14190 Sorted by residual: angle pdb=" C SER C 201 " pdb=" N ARG C 202 " pdb=" CA ARG C 202 " ideal model delta sigma weight residual 121.80 127.27 -5.47 2.44e+00 1.68e-01 5.02e+00 angle pdb=" C SER F 201 " pdb=" N ARG F 202 " pdb=" CA ARG F 202 " ideal model delta sigma weight residual 121.80 127.26 -5.46 2.44e+00 1.68e-01 5.01e+00 angle pdb=" C SER E 201 " pdb=" N ARG E 202 " pdb=" CA ARG E 202 " ideal model delta sigma weight residual 121.80 127.25 -5.45 2.44e+00 1.68e-01 4.99e+00 angle pdb=" C SER A 201 " pdb=" N ARG A 202 " pdb=" CA ARG A 202 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.98e+00 angle pdb=" C SER D 201 " pdb=" N ARG D 202 " pdb=" CA ARG D 202 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.98e+00 ... (remaining 14185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 6001 16.74 - 33.48: 283 33.48 - 50.22: 97 50.22 - 66.97: 24 66.97 - 83.71: 12 Dihedral angle restraints: 6417 sinusoidal: 2889 harmonic: 3528 Sorted by residual: dihedral pdb=" N PHE A 212 " pdb=" CA PHE A 212 " pdb=" CB PHE A 212 " pdb=" CG PHE A 212 " ideal model delta sinusoidal sigma weight residual 180.00 -126.50 -53.50 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" N PHE C 212 " pdb=" CA PHE C 212 " pdb=" CB PHE C 212 " pdb=" CG PHE C 212 " ideal model delta sinusoidal sigma weight residual -180.00 -126.52 -53.48 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" N PHE B 212 " pdb=" CA PHE B 212 " pdb=" CB PHE B 212 " pdb=" CG PHE B 212 " ideal model delta sinusoidal sigma weight residual -180.00 -126.53 -53.47 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 6414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 878 0.021 - 0.041: 409 0.041 - 0.062: 227 0.062 - 0.083: 53 0.083 - 0.103: 35 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CA PRO B 203 " pdb=" N PRO B 203 " pdb=" C PRO B 203 " pdb=" CB PRO B 203 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.66e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 chirality pdb=" CA VAL C 184 " pdb=" N VAL C 184 " pdb=" C VAL C 184 " pdb=" CB VAL C 184 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 1599 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 190 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01 pdb=" N PRO E 191 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO E 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO E 191 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 190 " -0.014 5.00e-02 4.00e+02 2.12e-02 7.20e-01 pdb=" N PRO C 191 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 190 " 0.014 5.00e-02 4.00e+02 2.12e-02 7.20e-01 pdb=" N PRO F 191 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO F 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 191 " 0.011 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 74 2.60 - 3.18: 8763 3.18 - 3.75: 15755 3.75 - 4.33: 18879 4.33 - 4.90: 32102 Nonbonded interactions: 75573 Sorted by model distance: nonbonded pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 61 " pdb=" SG CYS E 192 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS F 61 " pdb=" SG CYS F 192 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 61 " pdb=" SG CYS D 192 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 61 " pdb=" SG CYS C 192 " model vdw 2.032 3.760 ... (remaining 75568 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' } 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 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: 1.760 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.490 Find NCS groups from input model: 0.380 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.002 0.018 10476 Z= 0.126 Angle : 0.459 6.101 14190 Z= 0.234 Chirality : 0.032 0.103 1602 Planarity : 0.002 0.021 1674 Dihedral : 12.111 83.707 4128 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.52 % Favored : 97.97 % Rotamer: Outliers : 5.00 % Allowed : 3.89 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.98 (0.24), residues: 1182 helix: 2.75 (0.17), residues: 834 sheet: 3.07 (0.70), residues: 66 loop : -0.84 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 78 HIS 0.001 0.000 HIS F 194 PHE 0.006 0.001 PHE E 32 TYR 0.008 0.001 TYR C 155 ARG 0.001 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 1.088 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: A 47 ASP cc_start: 0.8362 (p0) cc_final: 0.8146 (p0) REVERT: A 173 GLN cc_start: 0.9564 (tt0) cc_final: 0.8945 (tm-30) REVERT: B 47 ASP cc_start: 0.8326 (p0) cc_final: 0.8049 (p0) REVERT: B 92 TYR cc_start: 0.9254 (t80) cc_final: 0.9052 (t80) REVERT: B 103 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9290 (mm-30) REVERT: B 173 GLN cc_start: 0.9582 (tt0) cc_final: 0.8986 (tm-30) REVERT: C 47 ASP cc_start: 0.8056 (p0) cc_final: 0.7758 (p0) REVERT: C 92 TYR cc_start: 0.9307 (t80) cc_final: 0.9097 (t80) REVERT: C 173 GLN cc_start: 0.9550 (tt0) cc_final: 0.9013 (tm-30) REVERT: D 47 ASP cc_start: 0.8142 (p0) cc_final: 0.7864 (p0) REVERT: D 103 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9096 (tp30) REVERT: E 47 ASP cc_start: 0.8197 (p0) cc_final: 0.7835 (p0) REVERT: E 101 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8595 (tpt170) REVERT: E 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.8998 (tm-30) REVERT: F 47 ASP cc_start: 0.8159 (p0) cc_final: 0.7887 (p0) REVERT: F 101 ARG cc_start: 0.8930 (mtp85) cc_final: 0.8688 (tpt170) REVERT: F 173 GLN cc_start: 0.9563 (tt0) cc_final: 0.9032 (tm-30) REVERT: F 202 ARG cc_start: 0.8823 (ptp-170) cc_final: 0.8540 (ptp90) outliers start: 54 outliers final: 19 residues processed: 340 average time/residue: 0.2638 time to fit residues: 118.4953 Evaluate side-chains 205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN C 49 GLN C 107 ASN C 224 ASN D 49 GLN D 224 ASN E 107 ASN E 224 ASN F 107 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10476 Z= 0.278 Angle : 0.654 8.628 14190 Z= 0.331 Chirality : 0.038 0.285 1602 Planarity : 0.004 0.028 1674 Dihedral : 11.509 86.522 1884 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.38 % Favored : 96.11 % Rotamer: Outliers : 3.89 % Allowed : 14.72 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.74 (0.24), residues: 1182 helix: 2.48 (0.17), residues: 846 sheet: 2.84 (0.69), residues: 66 loop : -0.71 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 45 HIS 0.003 0.001 HIS F 74 PHE 0.010 0.001 PHE E 212 TYR 0.010 0.001 TYR C 92 ARG 0.007 0.001 ARG E 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8298 (p0) cc_final: 0.8089 (p0) REVERT: A 173 GLN cc_start: 0.9619 (tt0) cc_final: 0.8988 (tm-30) REVERT: B 53 ARG cc_start: 0.8884 (ptp-110) cc_final: 0.8487 (mtm-85) REVERT: B 92 TYR cc_start: 0.9324 (t80) cc_final: 0.8734 (t80) REVERT: B 173 GLN cc_start: 0.9629 (tt0) cc_final: 0.9000 (tm-30) REVERT: C 92 TYR cc_start: 0.9367 (t80) cc_final: 0.8669 (t80) REVERT: C 173 GLN cc_start: 0.9617 (tt0) cc_final: 0.9040 (tm-30) REVERT: D 47 ASP cc_start: 0.8047 (p0) cc_final: 0.7832 (p0) REVERT: D 155 TYR cc_start: 0.8708 (t80) cc_final: 0.8340 (t80) REVERT: D 173 GLN cc_start: 0.9675 (tt0) cc_final: 0.9098 (tm-30) REVERT: E 48 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: E 61 CYS cc_start: 0.8875 (t) cc_final: 0.8425 (t) REVERT: E 101 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8636 (tpt170) REVERT: E 173 GLN cc_start: 0.9606 (tt0) cc_final: 0.9079 (tm-30) REVERT: F 101 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8735 (tpt170) REVERT: F 173 GLN cc_start: 0.9600 (tt0) cc_final: 0.9029 (tm-30) outliers start: 42 outliers final: 28 residues processed: 217 average time/residue: 0.2298 time to fit residues: 69.3540 Evaluate side-chains 194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN E 15 GLN E 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10476 Z= 0.210 Angle : 0.627 9.701 14190 Z= 0.315 Chirality : 0.036 0.230 1602 Planarity : 0.004 0.033 1674 Dihedral : 11.206 88.413 1884 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.03 % Favored : 97.46 % Rotamer: Outliers : 4.63 % Allowed : 15.37 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.72 (0.24), residues: 1182 helix: 2.60 (0.18), residues: 828 sheet: 2.86 (0.70), residues: 66 loop : -1.00 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 45 HIS 0.002 0.001 HIS C 194 PHE 0.006 0.001 PHE D 32 TYR 0.009 0.001 TYR A 66 ARG 0.003 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8439 (mt-10) REVERT: B 42 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 47 ASP cc_start: 0.8082 (p0) cc_final: 0.7836 (p0) REVERT: B 92 TYR cc_start: 0.9312 (t80) cc_final: 0.8715 (t80) REVERT: B 173 GLN cc_start: 0.9620 (tt0) cc_final: 0.9034 (tm-30) REVERT: C 92 TYR cc_start: 0.9357 (t80) cc_final: 0.8683 (t80) REVERT: C 166 GLU cc_start: 0.8740 (pp20) cc_final: 0.8539 (pp20) REVERT: C 173 GLN cc_start: 0.9610 (tt0) cc_final: 0.9018 (tm-30) REVERT: D 47 ASP cc_start: 0.8006 (p0) cc_final: 0.7802 (p0) REVERT: D 61 CYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8606 (t) REVERT: D 155 TYR cc_start: 0.8802 (t80) cc_final: 0.8475 (t80) REVERT: E 101 ARG cc_start: 0.8882 (mtp85) cc_final: 0.8629 (tpt170) REVERT: E 173 GLN cc_start: 0.9596 (tt0) cc_final: 0.9076 (tm-30) REVERT: F 101 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8713 (tpt170) REVERT: F 166 GLU cc_start: 0.8731 (pp20) cc_final: 0.8526 (pp20) REVERT: F 173 GLN cc_start: 0.9594 (tt0) cc_final: 0.9003 (tm-30) REVERT: F 205 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8332 (mt-10) outliers start: 50 outliers final: 37 residues processed: 223 average time/residue: 0.2246 time to fit residues: 71.8889 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN C 224 ASN D 224 ASN E 224 ASN F 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10476 Z= 0.257 Angle : 0.642 9.983 14190 Z= 0.327 Chirality : 0.037 0.227 1602 Planarity : 0.004 0.041 1674 Dihedral : 11.073 89.979 1884 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.05 % Favored : 96.45 % Rotamer: Outliers : 5.09 % Allowed : 15.83 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.61 (0.24), residues: 1182 helix: 2.44 (0.18), residues: 840 sheet: 2.69 (0.69), residues: 66 loop : -0.88 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 45 HIS 0.002 0.001 HIS E 194 PHE 0.008 0.001 PHE A 209 TYR 0.010 0.001 TYR A 92 ARG 0.005 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8113 (p0) cc_final: 0.7908 (p0) REVERT: B 47 ASP cc_start: 0.8097 (p0) cc_final: 0.7799 (p0) REVERT: B 61 CYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8741 (t) REVERT: B 92 TYR cc_start: 0.9339 (t80) cc_final: 0.8761 (t80) REVERT: C 92 TYR cc_start: 0.9379 (t80) cc_final: 0.8706 (t80) REVERT: D 61 CYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8758 (t) REVERT: D 192 CYS cc_start: 0.8478 (m) cc_final: 0.8182 (p) REVERT: E 101 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8631 (tpt170) REVERT: F 101 ARG cc_start: 0.8889 (mtp85) cc_final: 0.8648 (tpt170) outliers start: 55 outliers final: 40 residues processed: 200 average time/residue: 0.2163 time to fit residues: 62.2695 Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10476 Z= 0.194 Angle : 0.624 10.932 14190 Z= 0.314 Chirality : 0.036 0.221 1602 Planarity : 0.004 0.035 1674 Dihedral : 10.807 88.313 1884 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.20 % Favored : 97.29 % Rotamer: Outliers : 4.81 % Allowed : 17.31 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.55 (0.24), residues: 1182 helix: 2.48 (0.17), residues: 834 sheet: 2.63 (0.70), residues: 66 loop : -1.10 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP C 45 HIS 0.002 0.000 HIS B 194 PHE 0.008 0.001 PHE A 32 TYR 0.008 0.001 TYR A 66 ARG 0.007 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 1.218 Fit side-chains REVERT: A 47 ASP cc_start: 0.8074 (p0) cc_final: 0.7803 (p0) REVERT: B 42 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 47 ASP cc_start: 0.8112 (p0) cc_final: 0.7791 (p0) REVERT: B 61 CYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8696 (t) REVERT: B 92 TYR cc_start: 0.9325 (t80) cc_final: 0.8740 (t80) REVERT: B 187 CYS cc_start: 0.8329 (t) cc_final: 0.8093 (t) REVERT: B 192 CYS cc_start: 0.8319 (m) cc_final: 0.7891 (p) REVERT: B 205 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8516 (mt-10) REVERT: C 92 TYR cc_start: 0.9366 (t80) cc_final: 0.8731 (t80) REVERT: C 173 GLN cc_start: 0.9591 (tt0) cc_final: 0.9038 (tm-30) REVERT: C 187 CYS cc_start: 0.8400 (t) cc_final: 0.8022 (t) REVERT: D 61 CYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8657 (t) REVERT: D 155 TYR cc_start: 0.8859 (t80) cc_final: 0.8631 (t80) REVERT: E 101 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8642 (tpt170) REVERT: F 101 ARG cc_start: 0.8943 (mtp85) cc_final: 0.8704 (tpt170) outliers start: 52 outliers final: 37 residues processed: 210 average time/residue: 0.2148 time to fit residues: 64.1179 Evaluate side-chains 196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN E 224 ASN F 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10476 Z= 0.178 Angle : 0.618 11.581 14190 Z= 0.308 Chirality : 0.036 0.204 1602 Planarity : 0.004 0.038 1674 Dihedral : 10.474 86.370 1882 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.35 % Allowed : 17.69 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.54 (0.24), residues: 1182 helix: 2.52 (0.17), residues: 828 sheet: 3.44 (0.67), residues: 60 loop : -1.34 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 25 HIS 0.001 0.000 HIS D 194 PHE 0.008 0.001 PHE D 32 TYR 0.006 0.001 TYR E 66 ARG 0.003 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8118 (p0) cc_final: 0.7890 (p0) REVERT: A 173 GLN cc_start: 0.9573 (tt0) cc_final: 0.9074 (tm-30) REVERT: A 195 GLN cc_start: 0.9227 (mt0) cc_final: 0.8626 (pp30) REVERT: A 205 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8508 (mt-10) REVERT: B 47 ASP cc_start: 0.8113 (p0) cc_final: 0.7815 (p0) REVERT: B 61 CYS cc_start: 0.8899 (t) cc_final: 0.8683 (t) REVERT: B 173 GLN cc_start: 0.9595 (tt0) cc_final: 0.9086 (tm-30) REVERT: B 187 CYS cc_start: 0.8341 (t) cc_final: 0.8088 (t) REVERT: B 192 CYS cc_start: 0.8289 (m) cc_final: 0.7827 (p) REVERT: B 205 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8566 (mt-10) REVERT: C 55 ASN cc_start: 0.9387 (t0) cc_final: 0.8979 (t0) REVERT: C 92 TYR cc_start: 0.9327 (t80) cc_final: 0.8819 (t80) REVERT: C 173 GLN cc_start: 0.9547 (tt0) cc_final: 0.9025 (tm-30) REVERT: C 187 CYS cc_start: 0.8437 (t) cc_final: 0.8048 (t) REVERT: D 155 TYR cc_start: 0.8835 (t80) cc_final: 0.8591 (t80) REVERT: D 205 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8447 (mt-10) REVERT: E 101 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8668 (tpt170) REVERT: E 173 GLN cc_start: 0.9555 (tt0) cc_final: 0.9083 (tm-30) REVERT: E 205 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8442 (mt-10) REVERT: F 47 ASP cc_start: 0.8033 (p0) cc_final: 0.7791 (p0) REVERT: F 173 GLN cc_start: 0.9553 (tt0) cc_final: 0.9014 (tm-30) outliers start: 47 outliers final: 36 residues processed: 220 average time/residue: 0.2543 time to fit residues: 79.5969 Evaluate side-chains 204 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN E 194 HIS E 224 ASN F 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10476 Z= 0.288 Angle : 0.678 10.265 14190 Z= 0.344 Chirality : 0.038 0.207 1602 Planarity : 0.004 0.047 1674 Dihedral : 10.514 89.936 1882 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.17 % Allowed : 18.98 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.40 (0.24), residues: 1182 helix: 2.38 (0.17), residues: 834 sheet: 3.16 (0.65), residues: 60 loop : -1.28 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 45 HIS 0.002 0.001 HIS A 74 PHE 0.011 0.001 PHE E 169 TYR 0.010 0.001 TYR D 92 ARG 0.009 0.001 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8166 (p0) cc_final: 0.7923 (p0) REVERT: A 195 GLN cc_start: 0.9226 (mt0) cc_final: 0.8667 (pp30) REVERT: B 42 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8381 (tm-30) REVERT: B 47 ASP cc_start: 0.8143 (p0) cc_final: 0.7835 (p0) REVERT: B 61 CYS cc_start: 0.8958 (t) cc_final: 0.8717 (t) REVERT: B 187 CYS cc_start: 0.8402 (t) cc_final: 0.8162 (t) REVERT: B 192 CYS cc_start: 0.8362 (m) cc_final: 0.7848 (p) REVERT: C 92 TYR cc_start: 0.9361 (t80) cc_final: 0.8828 (t80) REVERT: C 187 CYS cc_start: 0.8324 (t) cc_final: 0.7969 (t) REVERT: D 205 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8580 (mt-10) REVERT: E 101 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8691 (tpt170) REVERT: E 205 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8565 (mt-10) outliers start: 45 outliers final: 37 residues processed: 189 average time/residue: 0.2111 time to fit residues: 57.6369 Evaluate side-chains 188 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10476 Z= 0.278 Angle : 0.692 10.155 14190 Z= 0.349 Chirality : 0.038 0.214 1602 Planarity : 0.004 0.052 1674 Dihedral : 10.421 89.824 1882 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.98 % Allowed : 19.81 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.34 (0.24), residues: 1182 helix: 2.39 (0.17), residues: 834 sheet: 2.89 (0.64), residues: 60 loop : -1.41 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 45 HIS 0.002 0.001 HIS E 194 PHE 0.009 0.001 PHE D 169 TYR 0.009 0.001 TYR D 92 ARG 0.012 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8214 (p0) cc_final: 0.7967 (p0) REVERT: A 195 GLN cc_start: 0.9178 (mt0) cc_final: 0.8710 (pp30) REVERT: B 47 ASP cc_start: 0.8165 (p0) cc_final: 0.7845 (p0) REVERT: B 48 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: B 61 CYS cc_start: 0.8962 (t) cc_final: 0.8731 (t) REVERT: B 192 CYS cc_start: 0.8440 (m) cc_final: 0.8054 (p) REVERT: C 92 TYR cc_start: 0.9350 (t80) cc_final: 0.8812 (t80) REVERT: C 187 CYS cc_start: 0.8350 (t) cc_final: 0.7982 (t) REVERT: D 187 CYS cc_start: 0.8395 (t) cc_final: 0.7799 (t) REVERT: D 205 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8596 (mt-10) REVERT: E 205 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8575 (mt-10) REVERT: F 187 CYS cc_start: 0.8157 (t) cc_final: 0.7538 (t) outliers start: 43 outliers final: 37 residues processed: 186 average time/residue: 0.2233 time to fit residues: 59.5443 Evaluate side-chains 185 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 CYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN E 224 ASN F 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10476 Z= 0.163 Angle : 0.679 9.748 14190 Z= 0.333 Chirality : 0.036 0.187 1602 Planarity : 0.004 0.053 1674 Dihedral : 10.262 89.639 1882 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.15 % Allowed : 20.56 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.40 (0.24), residues: 1182 helix: 2.46 (0.17), residues: 834 sheet: 3.09 (0.67), residues: 60 loop : -1.55 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 45 HIS 0.001 0.000 HIS D 194 PHE 0.009 0.001 PHE F 32 TYR 0.005 0.001 TYR C 92 ARG 0.009 0.001 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8201 (p0) cc_final: 0.7970 (p0) REVERT: A 173 GLN cc_start: 0.9540 (tt0) cc_final: 0.9073 (tm-30) REVERT: A 195 GLN cc_start: 0.9131 (mt0) cc_final: 0.8710 (pp30) REVERT: B 42 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8461 (tm-30) REVERT: B 47 ASP cc_start: 0.8101 (p0) cc_final: 0.7829 (p0) REVERT: B 173 GLN cc_start: 0.9560 (tt0) cc_final: 0.9078 (tm-30) REVERT: B 192 CYS cc_start: 0.8315 (m) cc_final: 0.8029 (p) REVERT: C 55 ASN cc_start: 0.9391 (t0) cc_final: 0.9012 (t0) REVERT: C 92 TYR cc_start: 0.9301 (t80) cc_final: 0.8762 (t80) REVERT: C 173 GLN cc_start: 0.9539 (tt0) cc_final: 0.9066 (tm-30) REVERT: C 187 CYS cc_start: 0.8271 (t) cc_final: 0.7894 (t) REVERT: D 92 TYR cc_start: 0.9425 (t80) cc_final: 0.8680 (t80) REVERT: D 195 GLN cc_start: 0.9193 (mt0) cc_final: 0.8704 (pp30) REVERT: D 205 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8507 (mt-10) REVERT: E 42 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8316 (tm-30) REVERT: E 173 GLN cc_start: 0.9548 (tt0) cc_final: 0.9084 (tm-30) REVERT: E 205 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8474 (mt-10) REVERT: F 173 GLN cc_start: 0.9540 (tt0) cc_final: 0.9048 (tm-30) REVERT: F 195 GLN cc_start: 0.9199 (mt0) cc_final: 0.8877 (pp30) outliers start: 34 outliers final: 31 residues processed: 210 average time/residue: 0.2127 time to fit residues: 63.8363 Evaluate side-chains 203 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 0.0370 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 overall best weight: 1.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN E 224 ASN F 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10476 Z= 0.196 Angle : 0.690 9.549 14190 Z= 0.343 Chirality : 0.036 0.185 1602 Planarity : 0.004 0.068 1674 Dihedral : 10.054 89.729 1874 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.43 % Allowed : 20.09 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.39 (0.24), residues: 1182 helix: 2.37 (0.17), residues: 852 sheet: 3.17 (0.68), residues: 60 loop : -1.53 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 45 HIS 0.001 0.000 HIS E 194 PHE 0.009 0.001 PHE D 32 TYR 0.006 0.001 TYR D 66 ARG 0.015 0.001 ARG A 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.242 Fit side-chains REVERT: A 47 ASP cc_start: 0.8210 (p0) cc_final: 0.7978 (p0) REVERT: A 173 GLN cc_start: 0.9532 (tt0) cc_final: 0.9077 (tm-30) REVERT: A 195 GLN cc_start: 0.9130 (mt0) cc_final: 0.8715 (pp30) REVERT: B 47 ASP cc_start: 0.8163 (p0) cc_final: 0.7892 (p0) REVERT: B 173 GLN cc_start: 0.9567 (tt0) cc_final: 0.9091 (tm-30) REVERT: B 187 CYS cc_start: 0.8349 (t) cc_final: 0.8086 (t) REVERT: B 192 CYS cc_start: 0.8435 (m) cc_final: 0.8000 (p) REVERT: C 55 ASN cc_start: 0.9393 (t0) cc_final: 0.9020 (t0) REVERT: C 92 TYR cc_start: 0.9334 (t80) cc_final: 0.8833 (t80) REVERT: C 173 GLN cc_start: 0.9533 (tt0) cc_final: 0.9074 (tm-30) REVERT: C 187 CYS cc_start: 0.8280 (t) cc_final: 0.7914 (t) REVERT: D 92 TYR cc_start: 0.9464 (t80) cc_final: 0.8714 (t80) REVERT: D 173 GLN cc_start: 0.9539 (tt0) cc_final: 0.9133 (tm-30) REVERT: D 195 GLN cc_start: 0.9187 (mt0) cc_final: 0.8696 (pp30) REVERT: D 205 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8546 (mt-10) REVERT: E 42 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 173 GLN cc_start: 0.9548 (tt0) cc_final: 0.9088 (tm-30) REVERT: E 205 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8516 (mt-10) REVERT: F 173 GLN cc_start: 0.9544 (tt0) cc_final: 0.9063 (tm-30) REVERT: F 187 CYS cc_start: 0.8225 (t) cc_final: 0.7638 (t) outliers start: 37 outliers final: 35 residues processed: 201 average time/residue: 0.2560 time to fit residues: 73.4864 Evaluate side-chains 205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN E 224 ASN F 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054245 restraints weight = 43681.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055929 restraints weight = 21875.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.057095 restraints weight = 14421.237| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10476 Z= 0.193 Angle : 0.709 9.271 14190 Z= 0.351 Chirality : 0.036 0.181 1602 Planarity : 0.004 0.056 1674 Dihedral : 10.007 89.747 1874 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.24 % Allowed : 20.83 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.39 (0.24), residues: 1182 helix: 2.39 (0.17), residues: 852 sheet: 3.14 (0.67), residues: 60 loop : -1.59 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 45 HIS 0.001 0.000 HIS E 194 PHE 0.009 0.001 PHE F 32 TYR 0.005 0.001 TYR C 92 ARG 0.009 0.001 ARG E 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.18 seconds wall clock time: 40 minutes 14.95 seconds (2414.95 seconds total)