Starting phenix.real_space_refine on Mon Jul 28 17:35:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqg_33395/07_2025/7xqg_33395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqg_33395/07_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_33395/07_2025/7xqg_33395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2025/7xqg_33395.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_2025/7xqg_33395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqg_33395/07_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-5711/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: 4.22, per 1000 atoms: 0.41 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=18, 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 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 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: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 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: 4.48 Time building geometry restraints manager: 3.83 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: 6026 16.74 - 33.48: 303 33.48 - 50.22: 97 50.22 - 66.97: 24 66.97 - 83.71: 12 Dihedral angle restraints: 6462 sinusoidal: 2934 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 6459 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: 2.27 - 2.79: 2430 2.79 - 3.32: 10217 3.32 - 3.85: 16371 3.85 - 4.37: 16449 4.37 - 4.90: 30061 Nonbonded interactions: 75528 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG1 THR C 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU F 35 " pdb=" OG1 THR F 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU D 35 " pdb=" OG1 THR D 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG1 THR A 39 " model vdw 2.268 3.040 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.268 3.040 ... (remaining 75523 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: 0.10 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: 1.180 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: 0.500 Check model and map are aligned: 0.170 Set scattering table: 0.150 Process input model: 32.090 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- 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 10494 Z= 0.099 Angle : 0.459 6.101 14226 Z= 0.234 Chirality : 0.032 0.103 1602 Planarity : 0.002 0.021 1674 Dihedral : 12.111 83.707 4128 Min Nonbonded Distance : 2.268 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 Details of bonding type rmsd hydrogen bonds : bond 0.08910 ( 702) hydrogen bonds : angle 2.97157 ( 2088) SS BOND : bond 0.00163 ( 18) SS BOND : angle 0.50849 ( 36) covalent geometry : bond 0.00197 (10476) covalent geometry : angle 0.45865 (14190) *********************** 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 : 1.317 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: 0.2614 time to fit residues: 117.6242 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 : 1.241 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.3345 r_free = 0.3345 target = 0.069872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.054320 restraints weight = 41651.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.056205 restraints weight = 20733.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057521 restraints weight = 13306.064| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10494 Z= 0.201 Angle : 0.755 10.013 14226 Z= 0.383 Chirality : 0.042 0.282 1602 Planarity : 0.004 0.027 1674 Dihedral : 11.593 86.440 1884 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.13 % Favored : 96.36 % Rotamer: Outliers : 4.72 % Allowed : 13.52 % Favored : 81.76 % 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: 2.44 (0.17), residues: 846 sheet: 2.29 (0.69), residues: 66 loop : -0.77 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 78 HIS 0.003 0.001 HIS F 74 PHE 0.009 0.001 PHE A 212 TYR 0.011 0.001 TYR D 66 ARG 0.006 0.001 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 702) hydrogen bonds : angle 3.16183 ( 2088) SS BOND : bond 0.00916 ( 18) SS BOND : angle 4.49110 ( 36) covalent geometry : bond 0.00484 (10476) covalent geometry : angle 0.72158 (14190) *********************** 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 230 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 1.125 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: A 47 ASP cc_start: 0.8248 (p0) cc_final: 0.8034 (p0) REVERT: A 173 GLN cc_start: 0.9614 (tt0) cc_final: 0.8972 (tm-30) REVERT: B 92 TYR cc_start: 0.9315 (t80) cc_final: 0.8715 (t80) REVERT: B 173 GLN cc_start: 0.9620 (tt0) cc_final: 0.8977 (tm-30) REVERT: C 92 TYR cc_start: 0.9339 (t80) cc_final: 0.8629 (t80) REVERT: C 173 GLN cc_start: 0.9610 (tt0) cc_final: 0.9029 (tm-30) REVERT: D 47 ASP cc_start: 0.8051 (p0) cc_final: 0.7841 (p0) REVERT: D 155 TYR cc_start: 0.8683 (t80) cc_final: 0.8288 (t80) REVERT: D 173 GLN cc_start: 0.9677 (tt0) cc_final: 0.9083 (tm-30) REVERT: E 48 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: E 101 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8673 (tpt170) REVERT: E 173 GLN cc_start: 0.9607 (tt0) cc_final: 0.9054 (tm-30) REVERT: F 53 ARG cc_start: 0.8873 (ptp-110) cc_final: 0.8657 (mtm110) REVERT: F 101 ARG cc_start: 0.9025 (mtp85) cc_final: 0.8782 (tpt170) REVERT: F 173 GLN cc_start: 0.9604 (tt0) cc_final: 0.9025 (tm-30) outliers start: 51 outliers final: 33 residues processed: 220 average time/residue: 0.2504 time to fit residues: 76.8495 Evaluate side-chains 194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 B residue 198 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 198 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 198 CYS 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 E residue 198 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 194 HIS Chi-restraints excluded: chain F residue 198 CYS 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: 0.9980 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.071138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055581 restraints weight = 41914.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057509 restraints weight = 20570.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058870 restraints weight = 12968.661| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10494 Z= 0.152 Angle : 0.719 12.037 14226 Z= 0.362 Chirality : 0.040 0.246 1602 Planarity : 0.004 0.033 1674 Dihedral : 11.267 88.285 1884 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.03 % Favored : 97.46 % Rotamer: Outliers : 4.72 % Allowed : 14.91 % Favored : 80.37 % 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: 2.52 (0.24), residues: 1182 helix: 2.59 (0.18), residues: 828 sheet: 1.81 (0.70), residues: 66 loop : -1.25 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 45 HIS 0.001 0.000 HIS B 194 PHE 0.007 0.001 PHE D 32 TYR 0.010 0.001 TYR C 66 ARG 0.004 0.000 ARG F 202 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 702) hydrogen bonds : angle 3.00752 ( 2088) SS BOND : bond 0.00847 ( 18) SS BOND : angle 3.74330 ( 36) covalent geometry : bond 0.00367 (10476) covalent geometry : angle 0.69476 (14190) *********************** 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 223 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9584 (tt0) cc_final: 0.8953 (tm-30) REVERT: B 42 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8362 (tm-30) REVERT: B 92 TYR cc_start: 0.9268 (t80) cc_final: 0.8678 (t80) REVERT: B 173 GLN cc_start: 0.9605 (tt0) cc_final: 0.9021 (tm-30) REVERT: C 92 TYR cc_start: 0.9302 (t80) cc_final: 0.8615 (t80) REVERT: C 173 GLN cc_start: 0.9581 (tt0) cc_final: 0.8991 (tm-30) REVERT: D 155 TYR cc_start: 0.8708 (t80) cc_final: 0.8362 (t80) REVERT: E 101 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8686 (tpt170) REVERT: E 173 GLN cc_start: 0.9578 (tt0) cc_final: 0.9045 (tm-30) REVERT: F 101 ARG cc_start: 0.8990 (mtp85) cc_final: 0.8760 (tpt170) REVERT: F 166 GLU cc_start: 0.8728 (pp20) cc_final: 0.8499 (pp20) REVERT: F 173 GLN cc_start: 0.9581 (tt0) cc_final: 0.8989 (tm-30) REVERT: F 205 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8334 (mt-10) outliers start: 51 outliers final: 37 residues processed: 217 average time/residue: 0.2729 time to fit residues: 84.4542 Evaluate side-chains 190 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 198 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 C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 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 198 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: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN E 224 ASN F 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.072427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.056762 restraints weight = 42043.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058679 restraints weight = 21102.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060091 restraints weight = 13427.198| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10494 Z= 0.138 Angle : 0.712 12.654 14226 Z= 0.355 Chirality : 0.039 0.225 1602 Planarity : 0.004 0.031 1674 Dihedral : 11.043 89.829 1884 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.62 % Favored : 96.87 % Rotamer: Outliers : 5.00 % Allowed : 15.37 % 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: 2.43 (0.24), residues: 1182 helix: 2.51 (0.18), residues: 834 sheet: 1.57 (0.71), residues: 66 loop : -1.28 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 45 HIS 0.001 0.000 HIS B 74 PHE 0.007 0.001 PHE A 32 TYR 0.010 0.001 TYR B 66 ARG 0.006 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 702) hydrogen bonds : angle 2.99406 ( 2088) SS BOND : bond 0.00861 ( 18) SS BOND : angle 3.30140 ( 36) covalent geometry : bond 0.00323 (10476) covalent geometry : angle 0.69343 (14190) *********************** 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 225 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9559 (tt0) cc_final: 0.8967 (tm-30) REVERT: B 92 TYR cc_start: 0.9278 (t80) cc_final: 0.8701 (t80) REVERT: B 173 GLN cc_start: 0.9586 (tt0) cc_final: 0.9045 (tm-30) REVERT: C 173 GLN cc_start: 0.9542 (tt0) cc_final: 0.8995 (tm-30) REVERT: D 47 ASP cc_start: 0.7790 (p0) cc_final: 0.7570 (p0) REVERT: D 155 TYR cc_start: 0.8700 (t80) cc_final: 0.8342 (t80) REVERT: E 42 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8306 (tm-30) REVERT: E 49 GLN cc_start: 0.8859 (tt0) cc_final: 0.8640 (mt0) REVERT: E 101 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8722 (tpt170) REVERT: E 173 GLN cc_start: 0.9553 (tt0) cc_final: 0.9052 (tm-30) REVERT: F 173 GLN cc_start: 0.9549 (tt0) cc_final: 0.8987 (tm-30) outliers start: 54 outliers final: 35 residues processed: 217 average time/residue: 0.2561 time to fit residues: 80.1254 Evaluate side-chains 191 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 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 198 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 Chi-restraints excluded: chain F residue 198 CYS 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: 3.9990 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056257 restraints weight = 42652.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058178 restraints weight = 21487.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059527 restraints weight = 13697.810| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10494 Z= 0.140 Angle : 0.725 11.592 14226 Z= 0.362 Chirality : 0.039 0.216 1602 Planarity : 0.004 0.041 1674 Dihedral : 10.833 87.426 1884 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.71 % Favored : 96.79 % Rotamer: Outliers : 4.72 % Allowed : 16.94 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.24), residues: 1182 helix: 2.49 (0.18), residues: 834 sheet: 1.17 (0.71), residues: 66 loop : -1.41 (0.30), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.000 TRP F 45 HIS 0.003 0.001 HIS E 194 PHE 0.008 0.001 PHE A 32 TYR 0.010 0.001 TYR A 66 ARG 0.006 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 702) hydrogen bonds : angle 3.05251 ( 2088) SS BOND : bond 0.00833 ( 18) SS BOND : angle 3.18576 ( 36) covalent geometry : bond 0.00330 (10476) covalent geometry : angle 0.70771 (14190) *********************** 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 217 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9541 (tt0) cc_final: 0.8994 (tm-30) REVERT: B 42 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 92 TYR cc_start: 0.9277 (t80) cc_final: 0.8705 (t80) REVERT: B 173 GLN cc_start: 0.9573 (tt0) cc_final: 0.9068 (tm-30) REVERT: B 205 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8568 (mt-10) REVERT: C 173 GLN cc_start: 0.9533 (tt0) cc_final: 0.8999 (tm-30) REVERT: D 47 ASP cc_start: 0.7881 (p0) cc_final: 0.7636 (p0) REVERT: D 155 TYR cc_start: 0.8732 (t80) cc_final: 0.8386 (t80) REVERT: E 49 GLN cc_start: 0.8873 (tt0) cc_final: 0.8652 (mt0) REVERT: E 101 ARG cc_start: 0.8978 (mtp85) cc_final: 0.8768 (tpt170) REVERT: E 173 GLN cc_start: 0.9532 (tt0) cc_final: 0.9046 (tm-30) REVERT: F 173 GLN cc_start: 0.9536 (tt0) cc_final: 0.8993 (tm-30) outliers start: 51 outliers final: 38 residues processed: 209 average time/residue: 0.2098 time to fit residues: 63.3524 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 224 ASN 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 C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 0.0770 overall best weight: 1.1940 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.072210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056514 restraints weight = 43013.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058430 restraints weight = 21759.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059776 restraints weight = 13971.713| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10494 Z= 0.134 Angle : 0.707 12.379 14226 Z= 0.350 Chirality : 0.039 0.222 1602 Planarity : 0.004 0.042 1674 Dihedral : 10.610 85.608 1884 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.35 % Allowed : 18.06 % 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: 2.29 (0.24), residues: 1182 helix: 2.53 (0.18), residues: 828 sheet: 1.59 (0.72), residues: 60 loop : -1.63 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP F 45 HIS 0.004 0.000 HIS C 194 PHE 0.008 0.001 PHE A 32 TYR 0.008 0.001 TYR C 66 ARG 0.007 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 702) hydrogen bonds : angle 3.03487 ( 2088) SS BOND : bond 0.00881 ( 18) SS BOND : angle 2.94252 ( 36) covalent geometry : bond 0.00309 (10476) covalent geometry : angle 0.69229 (14190) *********************** 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 217 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9514 (tt0) cc_final: 0.9004 (tm-30) REVERT: A 195 GLN cc_start: 0.9260 (mt0) cc_final: 0.8726 (pp30) REVERT: B 92 TYR cc_start: 0.9274 (t80) cc_final: 0.8679 (t80) REVERT: B 173 GLN cc_start: 0.9559 (tt0) cc_final: 0.9066 (tm-30) REVERT: C 173 GLN cc_start: 0.9524 (tt0) cc_final: 0.9044 (tm-30) REVERT: C 195 GLN cc_start: 0.9203 (mt0) cc_final: 0.8669 (pp30) REVERT: D 155 TYR cc_start: 0.8722 (t80) cc_final: 0.8382 (t80) REVERT: D 195 GLN cc_start: 0.9216 (mt0) cc_final: 0.8634 (pp30) REVERT: D 205 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8492 (mt-10) REVERT: E 173 GLN cc_start: 0.9519 (tt0) cc_final: 0.9093 (tm-30) REVERT: E 195 GLN cc_start: 0.9207 (mt0) cc_final: 0.8746 (pp30) REVERT: F 92 TYR cc_start: 0.9160 (t80) cc_final: 0.8777 (t80) REVERT: F 173 GLN cc_start: 0.9515 (tt0) cc_final: 0.9034 (tm-30) outliers start: 47 outliers final: 38 residues processed: 211 average time/residue: 0.2020 time to fit residues: 61.3230 Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 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 C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 67 ASP 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 198 CYS Chi-restraints excluded: chain F residue 67 ASP 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 Chi-restraints excluded: chain F residue 198 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 5.9990 chunk 101 optimal weight: 0.0060 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.072382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056662 restraints weight = 43370.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.058583 restraints weight = 21898.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059921 restraints weight = 14059.196| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10494 Z= 0.136 Angle : 0.730 11.413 14226 Z= 0.360 Chirality : 0.039 0.201 1602 Planarity : 0.004 0.050 1674 Dihedral : 10.477 89.944 1882 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.26 % Allowed : 17.87 % 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: 2.32 (0.24), residues: 1182 helix: 2.46 (0.17), residues: 852 sheet: 1.43 (0.74), residues: 60 loop : -1.62 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP F 45 HIS 0.001 0.000 HIS B 194 PHE 0.008 0.001 PHE F 32 TYR 0.008 0.001 TYR E 66 ARG 0.012 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 702) hydrogen bonds : angle 3.05363 ( 2088) SS BOND : bond 0.00836 ( 18) SS BOND : angle 2.79650 ( 36) covalent geometry : bond 0.00309 (10476) covalent geometry : angle 0.71713 (14190) *********************** 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 211 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.9212 (t80) cc_final: 0.8828 (t80) REVERT: A 173 GLN cc_start: 0.9506 (tt0) cc_final: 0.9048 (tm-30) REVERT: A 195 GLN cc_start: 0.9265 (mt0) cc_final: 0.8657 (pp30) REVERT: B 42 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 92 TYR cc_start: 0.9276 (t80) cc_final: 0.8677 (t80) REVERT: B 173 GLN cc_start: 0.9547 (tt0) cc_final: 0.9073 (tm-30) REVERT: B 205 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8539 (mp0) REVERT: C 173 GLN cc_start: 0.9504 (tt0) cc_final: 0.9026 (tm-30) REVERT: C 195 GLN cc_start: 0.9197 (mt0) cc_final: 0.8711 (pp30) REVERT: D 92 TYR cc_start: 0.9427 (t80) cc_final: 0.9219 (t80) REVERT: D 155 TYR cc_start: 0.8729 (t80) cc_final: 0.8427 (t80) REVERT: D 173 GLN cc_start: 0.9537 (tt0) cc_final: 0.9062 (tm-30) REVERT: D 195 GLN cc_start: 0.9226 (mt0) cc_final: 0.8390 (pp30) REVERT: D 205 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8464 (mt-10) REVERT: E 42 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8361 (tm-30) REVERT: E 173 GLN cc_start: 0.9509 (tt0) cc_final: 0.9099 (tm-30) REVERT: E 195 GLN cc_start: 0.9197 (mt0) cc_final: 0.8794 (pp30) REVERT: E 205 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8524 (mt-10) REVERT: F 92 TYR cc_start: 0.9160 (t80) cc_final: 0.8763 (t80) REVERT: F 173 GLN cc_start: 0.9521 (tt0) cc_final: 0.9032 (tm-30) REVERT: F 195 GLN cc_start: 0.9139 (mt0) cc_final: 0.8724 (pp30) outliers start: 46 outliers final: 37 residues processed: 207 average time/residue: 0.2359 time to fit residues: 69.7555 Evaluate side-chains 198 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS 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 C residue 198 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 67 ASP 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 198 CYS Chi-restraints excluded: chain F residue 67 ASP 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 Chi-restraints excluded: chain F residue 198 CYS 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: 0.9980 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.072845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.057194 restraints weight = 42782.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.059132 restraints weight = 21718.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060503 restraints weight = 13905.452| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10494 Z= 0.130 Angle : 0.732 10.823 14226 Z= 0.356 Chirality : 0.038 0.179 1602 Planarity : 0.004 0.047 1674 Dihedral : 10.304 89.911 1882 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: 2.28 (0.24), residues: 1182 helix: 2.42 (0.17), residues: 852 sheet: 1.31 (0.74), residues: 60 loop : -1.61 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP F 45 HIS 0.001 0.000 HIS D 194 PHE 0.008 0.001 PHE A 32 TYR 0.006 0.001 TYR C 66 ARG 0.014 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 702) hydrogen bonds : angle 3.03778 ( 2088) SS BOND : bond 0.00800 ( 18) SS BOND : angle 2.56995 ( 36) covalent geometry : bond 0.00293 (10476) covalent geometry : angle 0.72121 (14190) *********************** 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 206 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8065 (p0) cc_final: 0.7840 (p0) REVERT: A 92 TYR cc_start: 0.9233 (t80) cc_final: 0.8851 (t80) REVERT: A 173 GLN cc_start: 0.9469 (tt0) cc_final: 0.9057 (tm-30) REVERT: A 195 GLN cc_start: 0.9234 (mt0) cc_final: 0.8679 (pp30) REVERT: B 92 TYR cc_start: 0.9250 (t80) cc_final: 0.8646 (t80) REVERT: B 173 GLN cc_start: 0.9509 (tt0) cc_final: 0.9054 (tm-30) REVERT: B 195 GLN cc_start: 0.9127 (mt0) cc_final: 0.8516 (pp30) REVERT: B 205 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8483 (mp0) REVERT: C 173 GLN cc_start: 0.9482 (tt0) cc_final: 0.9038 (tm-30) REVERT: C 195 GLN cc_start: 0.9163 (mt0) cc_final: 0.8727 (pp30) REVERT: D 92 TYR cc_start: 0.9429 (t80) cc_final: 0.9229 (t80) REVERT: D 155 TYR cc_start: 0.8664 (t80) cc_final: 0.8346 (t80) REVERT: D 173 GLN cc_start: 0.9519 (tt0) cc_final: 0.9099 (tm-30) REVERT: D 195 GLN cc_start: 0.9166 (mt0) cc_final: 0.8438 (pp30) REVERT: D 205 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8424 (mt-10) REVERT: E 92 TYR cc_start: 0.9153 (t80) cc_final: 0.8709 (t80) REVERT: E 173 GLN cc_start: 0.9483 (tt0) cc_final: 0.9106 (tm-30) REVERT: E 195 GLN cc_start: 0.9140 (mt0) cc_final: 0.8777 (pp30) REVERT: F 92 TYR cc_start: 0.9176 (t80) cc_final: 0.8787 (t80) REVERT: F 173 GLN cc_start: 0.9478 (tt0) cc_final: 0.9025 (tm-30) REVERT: F 195 GLN cc_start: 0.9133 (mt0) cc_final: 0.8730 (pp30) outliers start: 36 outliers final: 33 residues processed: 204 average time/residue: 0.2522 time to fit residues: 74.3772 Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 HIS 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 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 224 ASN Chi-restraints excluded: chain E residue 67 ASP 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 198 CYS Chi-restraints excluded: chain F residue 67 ASP 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 198 CYS 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: 8.9990 chunk 100 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.072487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056825 restraints weight = 43136.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058731 restraints weight = 21838.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060061 restraints weight = 14117.926| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10494 Z= 0.139 Angle : 0.749 10.362 14226 Z= 0.369 Chirality : 0.039 0.177 1602 Planarity : 0.004 0.056 1674 Dihedral : 10.137 89.805 1878 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.24 % Allowed : 18.89 % 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: 2.23 (0.24), residues: 1182 helix: 2.39 (0.17), residues: 852 sheet: 1.35 (0.74), residues: 60 loop : -1.65 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP F 45 HIS 0.001 0.000 HIS B 74 PHE 0.008 0.001 PHE A 32 TYR 0.007 0.001 TYR D 66 ARG 0.014 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 702) hydrogen bonds : angle 3.06551 ( 2088) SS BOND : bond 0.00750 ( 18) SS BOND : angle 2.56443 ( 36) covalent geometry : bond 0.00321 (10476) covalent geometry : angle 0.73902 (14190) *********************** 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 200 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.9229 (t80) cc_final: 0.8839 (t80) REVERT: A 173 GLN cc_start: 0.9486 (tt0) cc_final: 0.9064 (tm-30) REVERT: A 195 GLN cc_start: 0.9236 (mt0) cc_final: 0.8668 (pp30) REVERT: B 92 TYR cc_start: 0.9288 (t80) cc_final: 0.8685 (t80) REVERT: B 173 GLN cc_start: 0.9527 (tt0) cc_final: 0.9065 (tm-30) REVERT: B 195 GLN cc_start: 0.9136 (mt0) cc_final: 0.8561 (pp30) REVERT: C 92 TYR cc_start: 0.9236 (t80) cc_final: 0.8779 (t80) REVERT: C 173 GLN cc_start: 0.9490 (tt0) cc_final: 0.9053 (tm-30) REVERT: C 195 GLN cc_start: 0.9154 (mt0) cc_final: 0.8722 (pp30) REVERT: D 155 TYR cc_start: 0.8721 (t80) cc_final: 0.8349 (t80) REVERT: D 173 GLN cc_start: 0.9532 (tt0) cc_final: 0.9101 (tm-30) REVERT: D 195 GLN cc_start: 0.9180 (mt0) cc_final: 0.8476 (pp30) REVERT: D 205 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8486 (mt-10) REVERT: E 92 TYR cc_start: 0.9164 (t80) cc_final: 0.8760 (t80) REVERT: E 173 GLN cc_start: 0.9491 (tt0) cc_final: 0.9107 (tm-30) REVERT: E 195 GLN cc_start: 0.9107 (mt0) cc_final: 0.8734 (pp30) REVERT: F 92 TYR cc_start: 0.9183 (t80) cc_final: 0.8780 (t80) REVERT: F 173 GLN cc_start: 0.9491 (tt0) cc_final: 0.9040 (tm-30) REVERT: F 195 GLN cc_start: 0.9108 (mt0) cc_final: 0.8726 (pp30) outliers start: 35 outliers final: 31 residues processed: 198 average time/residue: 0.2159 time to fit residues: 62.0347 Evaluate side-chains 193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain 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 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 224 ASN Chi-restraints excluded: chain E residue 67 ASP 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 67 ASP 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 198 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 0.0030 chunk 100 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.073281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.057748 restraints weight = 42942.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059702 restraints weight = 21983.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061027 restraints weight = 14076.941| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10494 Z= 0.136 Angle : 0.762 10.124 14226 Z= 0.374 Chirality : 0.038 0.179 1602 Planarity : 0.004 0.055 1674 Dihedral : 9.945 89.649 1874 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.96 % Allowed : 19.81 % Favored : 77.22 % 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: 2.15 (0.24), residues: 1182 helix: 2.35 (0.17), residues: 852 sheet: 1.27 (0.75), residues: 60 loop : -1.70 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP F 45 HIS 0.001 0.000 HIS E 194 PHE 0.009 0.001 PHE A 32 TYR 0.006 0.001 TYR D 66 ARG 0.013 0.001 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 702) hydrogen bonds : angle 3.07362 ( 2088) SS BOND : bond 0.00754 ( 18) SS BOND : angle 2.41313 ( 36) covalent geometry : bond 0.00308 (10476) covalent geometry : angle 0.75339 (14190) ********************** 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 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7979 (p0) cc_final: 0.7768 (p0) REVERT: A 92 TYR cc_start: 0.9222 (t80) cc_final: 0.8833 (t80) REVERT: A 103 GLU cc_start: 0.9145 (tp30) cc_final: 0.8811 (tm-30) REVERT: A 173 GLN cc_start: 0.9444 (tt0) cc_final: 0.9057 (tm-30) REVERT: A 195 GLN cc_start: 0.9226 (mt0) cc_final: 0.8676 (pp30) REVERT: B 92 TYR cc_start: 0.9253 (t80) cc_final: 0.8656 (t80) REVERT: B 173 GLN cc_start: 0.9496 (tt0) cc_final: 0.9095 (tm-30) REVERT: B 195 GLN cc_start: 0.9127 (mt0) cc_final: 0.8564 (pp30) REVERT: C 92 TYR cc_start: 0.9240 (t80) cc_final: 0.8817 (t80) REVERT: C 173 GLN cc_start: 0.9457 (tt0) cc_final: 0.9111 (tm-30) REVERT: C 195 GLN cc_start: 0.9128 (mt0) cc_final: 0.8685 (pp30) REVERT: D 42 GLU cc_start: 0.8682 (pp20) cc_final: 0.8114 (pt0) REVERT: D 155 TYR cc_start: 0.8693 (t80) cc_final: 0.8366 (t80) REVERT: D 173 GLN cc_start: 0.9510 (tt0) cc_final: 0.9121 (tm-30) REVERT: D 195 GLN cc_start: 0.9100 (mt0) cc_final: 0.8436 (pp30) REVERT: D 205 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8435 (mt-10) REVERT: E 42 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8494 (tm-30) REVERT: E 92 TYR cc_start: 0.9139 (t80) cc_final: 0.8762 (t80) REVERT: E 173 GLN cc_start: 0.9468 (tt0) cc_final: 0.9110 (tm-30) REVERT: E 195 GLN cc_start: 0.9067 (mt0) cc_final: 0.8750 (pp30) REVERT: F 92 TYR cc_start: 0.9191 (t80) cc_final: 0.8789 (t80) REVERT: F 173 GLN cc_start: 0.9463 (tt0) cc_final: 0.9053 (tm-30) REVERT: F 195 GLN cc_start: 0.9090 (mt0) cc_final: 0.8725 (pp30) REVERT: F 205 GLU cc_start: 0.8694 (pm20) cc_final: 0.8491 (pm20) outliers start: 32 outliers final: 27 residues processed: 198 average time/residue: 0.2056 time to fit residues: 58.2395 Evaluate side-chains 190 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 B residue 67 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 67 ASP 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 67 ASP 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: 8.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 0.0030 chunk 79 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 overall best weight: 2.1396 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.071693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056028 restraints weight = 43112.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057921 restraints weight = 22112.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.059237 restraints weight = 14308.218| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10494 Z= 0.158 Angle : 0.755 11.464 14226 Z= 0.375 Chirality : 0.039 0.208 1602 Planarity : 0.004 0.049 1674 Dihedral : 9.920 89.973 1872 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.96 % Allowed : 19.91 % 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: 2.04 (0.24), residues: 1182 helix: 2.19 (0.17), residues: 870 sheet: 1.27 (0.74), residues: 60 loop : -1.73 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 45 HIS 0.001 0.000 HIS B 74 PHE 0.007 0.001 PHE A 32 TYR 0.005 0.001 TYR D 92 ARG 0.012 0.001 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 702) hydrogen bonds : angle 3.12844 ( 2088) SS BOND : bond 0.00980 ( 18) SS BOND : angle 2.53117 ( 36) covalent geometry : bond 0.00365 (10476) covalent geometry : angle 0.74479 (14190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.33 seconds wall clock time: 63 minutes 26.19 seconds (3806.19 seconds total)