Starting phenix.real_space_refine on Fri Feb 14 19:16:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqg_33395/02_2025/7xqg_33395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqg_33395/02_2025/7xqg_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_33395/02_2025/7xqg_33395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqg_33395/02_2025/7xqg_33395.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqg_33395/02_2025/7xqg_33395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqg_33395/02_2025/7xqg_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-5592/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: 4.06, per 1000 atoms: 0.40 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: 2.74 Conformation dependent library (CDL) restraints added in 984.7 milliseconds 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: 0.79 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: 2.84 Time building geometry restraints manager: 3.10 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.320 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.300 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- 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 : 1.182 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: 0.2652 time to fit residues: 119.3729 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 : 1.102 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052749 restraints weight = 43165.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054472 restraints weight = 21434.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055678 restraints weight = 13794.232| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8288 (p0) cc_final: 0.8083 (p0) REVERT: A 173 GLN cc_start: 0.9613 (tt0) cc_final: 0.8977 (tm-30) REVERT: B 53 ARG cc_start: 0.8904 (ptp-110) cc_final: 0.8512 (mtm-85) REVERT: B 92 TYR cc_start: 0.9313 (t80) cc_final: 0.8715 (t80) REVERT: B 173 GLN cc_start: 0.9625 (tt0) cc_final: 0.8981 (tm-30) REVERT: C 92 TYR cc_start: 0.9341 (t80) cc_final: 0.8636 (t80) REVERT: C 173 GLN cc_start: 0.9615 (tt0) cc_final: 0.9034 (tm-30) REVERT: D 47 ASP cc_start: 0.8047 (p0) cc_final: 0.7836 (p0) REVERT: D 155 TYR cc_start: 0.8691 (t80) cc_final: 0.8326 (t80) REVERT: D 173 GLN cc_start: 0.9675 (tt0) cc_final: 0.9089 (tm-30) REVERT: E 48 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: E 61 CYS cc_start: 0.8820 (t) cc_final: 0.8369 (t) REVERT: E 101 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8678 (tpt170) REVERT: E 173 GLN cc_start: 0.9603 (tt0) cc_final: 0.9060 (tm-30) REVERT: F 101 ARG cc_start: 0.9024 (mtp85) cc_final: 0.8783 (tpt170) REVERT: F 173 GLN cc_start: 0.9600 (tt0) cc_final: 0.9027 (tm-30) outliers start: 42 outliers final: 28 residues processed: 217 average time/residue: 0.2222 time to fit residues: 67.3032 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 : 1.193 ------------------------------------------------------------------------------- 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 9 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.053655 restraints weight = 44004.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.055408 restraints weight = 21726.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.056632 restraints weight = 13862.748| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2449 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= 0.203 Angle : 0.627 9.675 14190 Z= 0.315 Chirality : 0.036 0.230 1602 Planarity : 0.004 0.032 1674 Dihedral : 11.216 88.146 1884 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.12 % Favored : 97.38 % Rotamer: Outliers : 4.44 % Allowed : 15.56 % 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: 2.73 (0.24), residues: 1182 helix: 2.61 (0.17), residues: 828 sheet: 2.84 (0.69), residues: 66 loop : -0.98 (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 0.007 0.001 PHE D 32 TYR 0.009 0.001 TYR A 66 ARG 0.004 0.000 ARG E 189 *********************** 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 234 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9592 (tt0) cc_final: 0.8976 (tm-30) REVERT: A 205 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8522 (mt-10) REVERT: B 47 ASP cc_start: 0.8054 (p0) cc_final: 0.7804 (p0) REVERT: B 61 CYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8452 (t) REVERT: B 92 TYR cc_start: 0.9301 (t80) cc_final: 0.8703 (t80) REVERT: B 173 GLN cc_start: 0.9608 (tt0) cc_final: 0.9005 (tm-30) REVERT: C 92 TYR cc_start: 0.9337 (t80) cc_final: 0.8655 (t80) REVERT: C 166 GLU cc_start: 0.8725 (pp20) cc_final: 0.8497 (pp20) REVERT: C 173 GLN cc_start: 0.9602 (tt0) cc_final: 0.9020 (tm-30) REVERT: D 61 CYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8600 (t) REVERT: D 155 TYR cc_start: 0.8748 (t80) cc_final: 0.8425 (t80) REVERT: E 101 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8667 (tpt170) REVERT: E 173 GLN cc_start: 0.9584 (tt0) cc_final: 0.9053 (tm-30) REVERT: F 101 ARG cc_start: 0.8984 (mtp85) cc_final: 0.8754 (tpt170) REVERT: F 166 GLU cc_start: 0.8714 (pp20) cc_final: 0.8488 (pp20) REVERT: F 173 GLN cc_start: 0.9589 (tt0) cc_final: 0.8995 (tm-30) REVERT: F 205 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8312 (mt-10) outliers start: 48 outliers final: 34 residues processed: 224 average time/residue: 0.2261 time to fit residues: 72.5463 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 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 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 119 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 106 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.070913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.055166 restraints weight = 43256.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056960 restraints weight = 21502.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058248 restraints weight = 13766.607| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10476 Z= 0.162 Angle : 0.628 10.392 14190 Z= 0.311 Chirality : 0.036 0.219 1602 Planarity : 0.004 0.038 1674 Dihedral : 10.948 89.926 1884 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.45 % Favored : 97.04 % Rotamer: Outliers : 4.54 % Allowed : 15.83 % Favored : 79.63 % 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: 2.62 (0.24), residues: 1182 helix: 2.53 (0.18), residues: 834 sheet: 2.78 (0.70), residues: 66 loop : -1.11 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 45 HIS 0.001 0.000 HIS E 194 PHE 0.008 0.001 PHE A 32 TYR 0.005 0.001 TYR A 155 ARG 0.006 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 232 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 1.109 Fit side-chains REVERT: A 173 GLN cc_start: 0.9551 (tt0) cc_final: 0.8965 (tm-30) REVERT: B 42 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8288 (tm-30) REVERT: B 55 ASN cc_start: 0.9389 (t0) cc_final: 0.9176 (t0) REVERT: B 61 CYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8639 (t) REVERT: B 92 TYR cc_start: 0.9261 (t80) cc_final: 0.8689 (t80) REVERT: B 173 GLN cc_start: 0.9578 (tt0) cc_final: 0.9036 (tm-30) REVERT: B 187 CYS cc_start: 0.8237 (t) cc_final: 0.8019 (t) REVERT: C 55 ASN cc_start: 0.9411 (t0) cc_final: 0.9145 (t0) REVERT: C 173 GLN cc_start: 0.9537 (tt0) cc_final: 0.8995 (tm-30) REVERT: D 47 ASP cc_start: 0.7778 (p0) cc_final: 0.7562 (p0) REVERT: D 61 CYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8626 (t) REVERT: D 155 TYR cc_start: 0.8702 (t80) cc_final: 0.8354 (t80) REVERT: D 192 CYS cc_start: 0.8410 (m) cc_final: 0.8188 (p) REVERT: E 42 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8309 (tm-30) REVERT: E 101 ARG cc_start: 0.8940 (mtp85) cc_final: 0.8724 (tpt170) REVERT: E 173 GLN cc_start: 0.9542 (tt0) cc_final: 0.9046 (tm-30) REVERT: F 173 GLN cc_start: 0.9541 (tt0) cc_final: 0.8984 (tm-30) outliers start: 49 outliers final: 35 residues processed: 220 average time/residue: 0.2052 time to fit residues: 64.7194 Evaluate side-chains 208 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 98 TYR 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 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 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 194 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.2164 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3351 r_free = 0.3351 target = 0.069497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.053838 restraints weight = 43664.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055542 restraints weight = 22061.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056772 restraints weight = 14439.735| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2767 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= 0.209 Angle : 0.634 10.816 14190 Z= 0.317 Chirality : 0.036 0.221 1602 Planarity : 0.004 0.038 1674 Dihedral : 10.773 87.544 1884 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.71 % Favored : 96.79 % Rotamer: Outliers : 4.72 % Allowed : 17.31 % 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: 2.65 (0.24), residues: 1182 helix: 2.47 (0.17), residues: 852 sheet: 2.75 (0.71), residues: 66 loop : -1.05 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 45 HIS 0.002 0.001 HIS A 194 PHE 0.009 0.001 PHE A 169 TYR 0.007 0.001 TYR A 92 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 223 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9548 (tt0) cc_final: 0.9001 (tm-30) REVERT: B 92 TYR cc_start: 0.9317 (t80) cc_final: 0.8741 (t80) REVERT: B 173 GLN cc_start: 0.9580 (tt0) cc_final: 0.9081 (tm-30) REVERT: B 187 CYS cc_start: 0.8310 (t) cc_final: 0.8097 (t) REVERT: B 192 CYS cc_start: 0.8178 (m) cc_final: 0.7795 (p) REVERT: B 205 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8553 (mp0) REVERT: C 55 ASN cc_start: 0.9403 (t0) cc_final: 0.8991 (t0) REVERT: C 173 GLN cc_start: 0.9541 (tt0) cc_final: 0.9009 (tm-30) REVERT: D 47 ASP cc_start: 0.7871 (p0) cc_final: 0.7628 (p0) REVERT: D 61 CYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8616 (t) REVERT: D 155 TYR cc_start: 0.8795 (t80) cc_final: 0.8484 (t80) REVERT: D 192 CYS cc_start: 0.8463 (m) cc_final: 0.8163 (p) REVERT: E 53 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8604 (mtm-85) REVERT: E 101 ARG cc_start: 0.8946 (mtp85) cc_final: 0.8744 (tpt170) REVERT: E 173 GLN cc_start: 0.9555 (tt0) cc_final: 0.9068 (tm-30) REVERT: F 173 GLN cc_start: 0.9546 (tt0) cc_final: 0.9002 (tm-30) outliers start: 51 outliers final: 38 residues processed: 211 average time/residue: 0.2015 time to fit residues: 61.1098 Evaluate side-chains 206 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS 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 212 PHE 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 B residue 224 ASN 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 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 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 17 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.055023 restraints weight = 43284.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056814 restraints weight = 21570.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058024 restraints weight = 13837.423| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2887 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= 0.160 Angle : 0.627 11.956 14190 Z= 0.309 Chirality : 0.036 0.192 1602 Planarity : 0.003 0.034 1674 Dihedral : 10.459 85.999 1882 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.98 % Allowed : 18.70 % Favored : 77.31 % 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: 2.62 (0.24), residues: 1182 helix: 2.53 (0.17), residues: 846 sheet: 3.43 (0.66), residues: 60 loop : -1.38 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP F 45 HIS 0.001 0.000 HIS D 194 PHE 0.009 0.001 PHE A 32 TYR 0.008 0.001 TYR A 66 ARG 0.008 0.000 ARG F 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: 43 poor density : 189 time to evaluate : 1.218 Fit side-chains REVERT: A 173 GLN cc_start: 0.9508 (tt0) cc_final: 0.9001 (tm-30) REVERT: A 195 GLN cc_start: 0.9270 (mt0) cc_final: 0.8650 (pp30) REVERT: A 205 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8566 (mt-10) REVERT: B 42 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8286 (tm-30) REVERT: B 92 TYR cc_start: 0.9274 (t80) cc_final: 0.8685 (t80) REVERT: B 173 GLN cc_start: 0.9558 (tt0) cc_final: 0.9056 (tm-30) REVERT: B 205 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8565 (mp0) REVERT: C 48 GLU cc_start: 0.7888 (mp0) cc_final: 0.7682 (mp0) REVERT: C 55 ASN cc_start: 0.9389 (t0) cc_final: 0.9115 (t0) REVERT: C 61 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7881 (t) REVERT: C 173 GLN cc_start: 0.9519 (tt0) cc_final: 0.9027 (tm-30) REVERT: D 47 ASP cc_start: 0.7908 (p0) cc_final: 0.7652 (p0) REVERT: D 61 CYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8633 (t) REVERT: D 92 TYR cc_start: 0.9429 (t80) cc_final: 0.9219 (t80) REVERT: D 155 TYR cc_start: 0.8730 (t80) cc_final: 0.8446 (t80) REVERT: D 192 CYS cc_start: 0.8302 (m) cc_final: 0.8100 (p) REVERT: D 205 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8488 (mt-10) REVERT: E 42 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8308 (tm-30) REVERT: E 173 GLN cc_start: 0.9520 (tt0) cc_final: 0.9083 (tm-30) REVERT: F 92 TYR cc_start: 0.9145 (t80) cc_final: 0.8773 (t80) REVERT: F 173 GLN cc_start: 0.9510 (tt0) cc_final: 0.8996 (tm-30) outliers start: 43 outliers final: 27 residues processed: 219 average time/residue: 0.2058 time to fit residues: 64.9031 Evaluate side-chains 200 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 0.0770 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN E 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054698 restraints weight = 44063.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056460 restraints weight = 22049.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.057688 restraints weight = 14367.834| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10476 Z= 0.181 Angle : 0.645 10.579 14190 Z= 0.318 Chirality : 0.036 0.186 1602 Planarity : 0.004 0.040 1674 Dihedral : 10.213 89.908 1872 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.33 % Allowed : 19.07 % Favored : 77.59 % 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: 2.60 (0.24), residues: 1182 helix: 2.47 (0.17), residues: 852 sheet: 3.49 (0.67), residues: 60 loop : -1.33 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 45 HIS 0.002 0.000 HIS F 194 PHE 0.008 0.001 PHE F 32 TYR 0.007 0.001 TYR A 155 ARG 0.008 0.001 ARG E 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 209 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.130 Fit side-chains REVERT: A 47 ASP cc_start: 0.8154 (p0) cc_final: 0.7942 (p0) REVERT: A 173 GLN cc_start: 0.9513 (tt0) cc_final: 0.9058 (tm-30) REVERT: A 195 GLN cc_start: 0.9256 (mt0) cc_final: 0.8670 (pp30) REVERT: B 92 TYR cc_start: 0.9302 (t80) cc_final: 0.8706 (t80) REVERT: B 173 GLN cc_start: 0.9559 (tt0) cc_final: 0.9082 (tm-30) REVERT: B 192 CYS cc_start: 0.8157 (m) cc_final: 0.7933 (p) REVERT: B 205 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8556 (mp0) REVERT: C 55 ASN cc_start: 0.9380 (t0) cc_final: 0.9012 (t0) REVERT: C 173 GLN cc_start: 0.9504 (tt0) cc_final: 0.9026 (tm-30) REVERT: D 47 ASP cc_start: 0.7912 (p0) cc_final: 0.7635 (p0) REVERT: D 155 TYR cc_start: 0.8782 (t80) cc_final: 0.8458 (t80) REVERT: D 205 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8475 (mt-10) REVERT: E 42 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8350 (tm-30) REVERT: E 173 GLN cc_start: 0.9511 (tt0) cc_final: 0.9095 (tm-30) REVERT: E 205 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8473 (mt-10) REVERT: F 61 CYS cc_start: 0.8468 (t) cc_final: 0.7533 (t) REVERT: F 92 TYR cc_start: 0.9195 (t80) cc_final: 0.8797 (t80) REVERT: F 173 GLN cc_start: 0.9505 (tt0) cc_final: 0.9017 (tm-30) outliers start: 36 outliers final: 30 residues processed: 203 average time/residue: 0.1961 time to fit residues: 58.0544 Evaluate side-chains 202 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN F 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.054232 restraints weight = 43568.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055978 restraints weight = 22287.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057187 restraints weight = 14481.809| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3059 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= 0.198 Angle : 0.658 9.752 14190 Z= 0.325 Chirality : 0.036 0.193 1602 Planarity : 0.004 0.053 1674 Dihedral : 10.107 89.791 1872 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.33 % Allowed : 18.80 % 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: 2.49 (0.24), residues: 1182 helix: 2.48 (0.17), residues: 834 sheet: 3.52 (0.67), residues: 60 loop : -1.44 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 45 HIS 0.001 0.000 HIS D 194 PHE 0.008 0.001 PHE F 32 TYR 0.007 0.001 TYR A 92 ARG 0.013 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 205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.193 Fit side-chains REVERT: A 173 GLN cc_start: 0.9527 (tt0) cc_final: 0.9065 (tm-30) REVERT: A 195 GLN cc_start: 0.9265 (mt0) cc_final: 0.8619 (pp30) REVERT: B 92 TYR cc_start: 0.9313 (t80) cc_final: 0.8711 (t80) REVERT: B 173 GLN cc_start: 0.9553 (tt0) cc_final: 0.9066 (tm-30) REVERT: B 205 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8574 (mt-10) REVERT: C 55 ASN cc_start: 0.9400 (t0) cc_final: 0.9049 (t0) REVERT: C 173 GLN cc_start: 0.9513 (tt0) cc_final: 0.9033 (tm-30) REVERT: C 187 CYS cc_start: 0.8331 (t) cc_final: 0.7960 (t) REVERT: D 155 TYR cc_start: 0.8809 (t80) cc_final: 0.8505 (t80) REVERT: D 205 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8516 (mt-10) REVERT: E 173 GLN cc_start: 0.9534 (tt0) cc_final: 0.9108 (tm-30) REVERT: E 205 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8516 (mt-10) REVERT: F 173 GLN cc_start: 0.9516 (tt0) cc_final: 0.9039 (tm-30) outliers start: 36 outliers final: 30 residues processed: 198 average time/residue: 0.1991 time to fit residues: 57.2415 Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054934 restraints weight = 43495.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056672 restraints weight = 22063.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.057887 restraints weight = 14505.828| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10476 Z= 0.171 Angle : 0.681 9.306 14190 Z= 0.333 Chirality : 0.036 0.185 1602 Planarity : 0.004 0.048 1674 Dihedral : 9.956 89.757 1872 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.06 % Allowed : 19.17 % Favored : 77.78 % 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: 2.48 (0.24), residues: 1182 helix: 2.49 (0.17), residues: 834 sheet: 3.55 (0.67), residues: 60 loop : -1.54 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 45 HIS 0.001 0.000 HIS B 194 PHE 0.008 0.001 PHE A 32 TYR 0.005 0.001 TYR A 66 ARG 0.009 0.000 ARG E 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 210 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 1.170 Fit side-chains REVERT: A 173 GLN cc_start: 0.9487 (tt0) cc_final: 0.9071 (tm-30) REVERT: A 195 GLN cc_start: 0.9174 (mt0) cc_final: 0.8631 (pp30) REVERT: B 42 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8366 (tm-30) REVERT: B 92 TYR cc_start: 0.9307 (t80) cc_final: 0.8703 (t80) REVERT: B 173 GLN cc_start: 0.9526 (tt0) cc_final: 0.9070 (tm-30) REVERT: B 205 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8584 (mp0) REVERT: C 55 ASN cc_start: 0.9374 (t0) cc_final: 0.9023 (t0) REVERT: C 92 TYR cc_start: 0.9262 (t80) cc_final: 0.8828 (t80) REVERT: C 173 GLN cc_start: 0.9492 (tt0) cc_final: 0.9056 (tm-30) REVERT: C 187 CYS cc_start: 0.8319 (t) cc_final: 0.7953 (t) REVERT: D 48 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7958 (mp0) REVERT: D 155 TYR cc_start: 0.8790 (t80) cc_final: 0.8457 (t80) REVERT: D 173 GLN cc_start: 0.9516 (tt0) cc_final: 0.9078 (tm-30) REVERT: D 205 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8483 (mt-10) REVERT: E 173 GLN cc_start: 0.9504 (tt0) cc_final: 0.9109 (tm-30) REVERT: E 205 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8472 (mt-10) REVERT: F 61 CYS cc_start: 0.8337 (t) cc_final: 0.7351 (t) REVERT: F 92 TYR cc_start: 0.9205 (t80) cc_final: 0.8789 (t80) REVERT: F 173 GLN cc_start: 0.9491 (tt0) cc_final: 0.9052 (tm-30) REVERT: F 195 GLN cc_start: 0.9139 (mt0) cc_final: 0.8830 (pp30) outliers start: 33 outliers final: 31 residues processed: 204 average time/residue: 0.1982 time to fit residues: 58.7449 Evaluate side-chains 204 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 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 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 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 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 24 optimal weight: 7.9990 chunk 44 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.055051 restraints weight = 43628.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056836 restraints weight = 22087.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058096 restraints weight = 14288.694| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3236 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= 0.179 Angle : 0.697 9.293 14190 Z= 0.338 Chirality : 0.036 0.182 1602 Planarity : 0.004 0.054 1674 Dihedral : 9.891 89.781 1872 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.78 % Allowed : 20.09 % Favored : 77.13 % 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: 2.43 (0.24), residues: 1182 helix: 2.48 (0.17), residues: 834 sheet: 3.47 (0.66), residues: 60 loop : -1.59 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 45 HIS 0.002 0.000 HIS E 194 PHE 0.008 0.001 PHE A 32 TYR 0.006 0.001 TYR A 66 ARG 0.009 0.001 ARG F 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 203 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.222 Fit side-chains REVERT: A 173 GLN cc_start: 0.9487 (tt0) cc_final: 0.9059 (tm-30) REVERT: A 195 GLN cc_start: 0.9190 (mt0) cc_final: 0.8643 (pp30) REVERT: B 42 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 92 TYR cc_start: 0.9295 (t80) cc_final: 0.8701 (t80) REVERT: B 173 GLN cc_start: 0.9538 (tt0) cc_final: 0.9060 (tm-30) REVERT: B 205 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8589 (mp0) REVERT: C 55 ASN cc_start: 0.9400 (t0) cc_final: 0.9076 (t0) REVERT: C 92 TYR cc_start: 0.9229 (t80) cc_final: 0.8801 (t80) REVERT: C 173 GLN cc_start: 0.9504 (tt0) cc_final: 0.9058 (tm-30) REVERT: C 187 CYS cc_start: 0.8355 (t) cc_final: 0.7967 (t) REVERT: D 155 TYR cc_start: 0.8773 (t80) cc_final: 0.8445 (t80) REVERT: D 173 GLN cc_start: 0.9531 (tt0) cc_final: 0.9069 (tm-30) REVERT: D 205 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8526 (mt-10) REVERT: E 61 CYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7788 (t) REVERT: E 173 GLN cc_start: 0.9509 (tt0) cc_final: 0.9095 (tm-30) REVERT: E 205 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8521 (mt-10) REVERT: F 92 TYR cc_start: 0.9166 (t80) cc_final: 0.8753 (t80) REVERT: F 173 GLN cc_start: 0.9501 (tt0) cc_final: 0.9051 (tm-30) REVERT: F 195 GLN cc_start: 0.9187 (mt0) cc_final: 0.8843 (pp30) outliers start: 30 outliers final: 29 residues processed: 198 average time/residue: 0.2010 time to fit residues: 57.7362 Evaluate side-chains 200 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 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 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 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 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 78 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054588 restraints weight = 43766.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056305 restraints weight = 22257.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057495 restraints weight = 14643.133| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10476 Z= 0.206 Angle : 0.687 9.286 14190 Z= 0.340 Chirality : 0.036 0.188 1602 Planarity : 0.004 0.056 1674 Dihedral : 9.855 89.806 1872 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.96 % Allowed : 20.00 % Favored : 77.04 % 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: 2.48 (0.24), residues: 1182 helix: 2.51 (0.17), residues: 834 sheet: 3.50 (0.67), residues: 60 loop : -1.58 (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 B 74 PHE 0.008 0.001 PHE A 32 TYR 0.006 0.001 TYR D 92 ARG 0.009 0.001 ARG F 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2735.15 seconds wall clock time: 50 minutes 26.88 seconds (3026.88 seconds total)