Starting phenix.real_space_refine on Tue Sep 24 01:09:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/09_2024/7e1e_30939.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/09_2024/7e1e_30939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/09_2024/7e1e_30939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/09_2024/7e1e_30939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/09_2024/7e1e_30939.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1e_30939/09_2024/7e1e_30939.cif" } resolution = 3.34 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= 0.001 sd= 0.009 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 Ca 6 9.91 5 S 36 5.16 5 C 4128 2.51 5 N 1092 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6489 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "B" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "C" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.35, per 1000 atoms: 0.67 Number of scatterers: 6489 At special positions: 0 Unit cell: (91.4578, 87.5382, 78.3924, 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) Ca 6 19.99 S 36 16.00 O 1227 8.00 N 1092 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 85 " distance=2.02 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 85 " distance=2.02 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 299 " distance=2.02 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 278 " distance=2.04 Simple disulfide: pdb=" SG CYS B 242 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 85 " distance=2.02 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 299 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 278 " distance=2.04 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 284 " 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: 1.58 Conformation dependent library (CDL) restraints added in 915.3 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 24.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 4.141A pdb=" N GLY A 91 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.019A pdb=" N LEU A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 247' Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.837A pdb=" N HIS A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'B' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 4.142A pdb=" N GLY B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.018A pdb=" N LEU B 246 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 242 through 247' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.836A pdb=" N HIS B 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 4.141A pdb=" N GLY C 91 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.020A pdb=" N LEU C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.836A pdb=" N HIS C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 74 removed outlier: 25.097A pdb=" N PHE A 80 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL A 100 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN A 82 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA A 98 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 25.097A pdb=" N PHE A 80 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL A 100 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN A 82 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA A 98 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 329 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 99 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 327 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE A 164 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 184 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG A 185 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 267 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 259 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE B 80 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL B 100 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN B 82 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA B 98 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE B 80 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL B 100 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN B 82 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA B 98 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 329 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER B 99 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 327 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE B 164 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 184 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG B 185 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 267 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 259 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE C 80 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL C 100 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 13.345A pdb=" N GLN C 82 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA C 98 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE C 80 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL C 100 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 13.345A pdb=" N GLN C 82 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA C 98 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 329 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER C 99 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 327 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE C 164 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 184 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG C 185 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 267 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE C 259 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 249 through 251 201 hydrogen bonds defined for protein. 486 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: 1.80 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2106 1.34 - 1.47: 1823 1.47 - 1.59: 2701 1.59 - 1.71: 0 1.71 - 1.83: 39 Bond restraints: 6669 Sorted by residual: bond pdb=" CB PHE C 184 " pdb=" CG PHE C 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.96e+00 bond pdb=" CB PHE A 184 " pdb=" CG PHE A 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.92e+00 bond pdb=" CB PHE B 184 " pdb=" CG PHE B 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.90e+00 bond pdb=" C TYR C 208 " pdb=" O TYR C 208 " ideal model delta sigma weight residual 1.240 1.223 0.017 1.24e-02 6.50e+03 1.78e+00 bond pdb=" C TYR A 208 " pdb=" O TYR A 208 " ideal model delta sigma weight residual 1.240 1.223 0.016 1.24e-02 6.50e+03 1.76e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8489 1.61 - 3.22: 507 3.22 - 4.84: 70 4.84 - 6.45: 15 6.45 - 8.06: 3 Bond angle restraints: 9084 Sorted by residual: angle pdb=" CA CYS C 242 " pdb=" CB CYS C 242 " pdb=" SG CYS C 242 " ideal model delta sigma weight residual 114.40 122.46 -8.06 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS B 242 " pdb=" CB CYS B 242 " pdb=" SG CYS B 242 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS A 242 " pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CB GLN B 177 " pdb=" CG GLN B 177 " pdb=" CD GLN B 177 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" CB GLN C 177 " pdb=" CG GLN C 177 " pdb=" CD GLN C 177 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.70e+00 3.46e-01 1.08e+01 ... (remaining 9079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 3573 25.96 - 51.93: 234 51.93 - 77.89: 42 77.89 - 103.85: 6 103.85 - 129.82: 3 Dihedral angle restraints: 3858 sinusoidal: 1476 harmonic: 2382 Sorted by residual: dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N TYR C 208 " pdb=" CA TYR C 208 " ideal model delta harmonic sigma weight residual 180.00 50.18 129.82 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N TYR A 208 " pdb=" CA TYR A 208 " ideal model delta harmonic sigma weight residual 180.00 50.20 129.80 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N TYR B 208 " pdb=" CA TYR B 208 " ideal model delta harmonic sigma weight residual 180.00 50.24 129.76 0 5.00e+00 4.00e-02 6.73e+02 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 543 0.037 - 0.074: 278 0.074 - 0.111: 118 0.111 - 0.148: 12 0.148 - 0.185: 6 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA VAL C 258 " pdb=" N VAL C 258 " pdb=" C VAL C 258 " pdb=" CB VAL C 258 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA VAL B 258 " pdb=" N VAL B 258 " pdb=" C VAL B 258 " pdb=" CB VAL B 258 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA VAL A 258 " pdb=" N VAL A 258 " pdb=" C VAL A 258 " pdb=" CB VAL A 258 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 954 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 217 " 0.063 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A 218 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 217 " -0.063 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO B 218 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 217 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO C 218 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 218 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 218 " 0.051 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 385 2.70 - 3.25: 6803 3.25 - 3.80: 11014 3.80 - 4.35: 14816 4.35 - 4.90: 24438 Nonbonded interactions: 57456 Sorted by model distance: nonbonded pdb=" O LYS C 62 " pdb=" NZ LYS C 64 " model vdw 2.154 3.120 nonbonded pdb=" O LYS A 62 " pdb=" NZ LYS A 64 " model vdw 2.155 3.120 nonbonded pdb=" O LYS B 62 " pdb=" NZ LYS B 64 " model vdw 2.155 3.120 nonbonded pdb=" OG SER A 77 " pdb=" OE2 GLU B 144 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP B 149 " pdb=" N ASP B 150 " model vdw 2.187 3.120 ... (remaining 57451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.790 Find NCS groups from input model: 0.240 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.007 0.039 6669 Z= 0.479 Angle : 0.858 8.062 9084 Z= 0.502 Chirality : 0.050 0.185 957 Planarity : 0.007 0.095 1188 Dihedral : 17.656 129.817 2307 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.03 % Favored : 90.61 % Rotamer: Outliers : 11.79 % Allowed : 5.82 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 15.38 % Twisted General : 0.38 % 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: -3.79 (0.23), residues: 831 helix: -3.33 (0.39), residues: 96 sheet: -1.21 (0.48), residues: 96 loop : -2.85 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 178 HIS 0.003 0.001 HIS B 101 PHE 0.015 0.002 PHE C 127 TYR 0.012 0.002 TYR C 201 ARG 0.015 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 171 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8410 (m-40) cc_final: 0.8200 (m110) REVERT: A 305 PHE cc_start: 0.8203 (m-10) cc_final: 0.7900 (m-10) REVERT: B 202 PHE cc_start: 0.7975 (m-80) cc_final: 0.7761 (m-10) REVERT: B 307 TRP cc_start: 0.6919 (t-100) cc_final: 0.6679 (t-100) REVERT: B 321 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8808 (t) REVERT: C 314 VAL cc_start: 0.6846 (OUTLIER) cc_final: 0.6635 (m) REVERT: C 320 LYS cc_start: 0.8542 (tttm) cc_final: 0.8329 (ttmm) outliers start: 81 outliers final: 13 residues processed: 227 average time/residue: 0.2092 time to fit residues: 60.5776 Evaluate side-chains 118 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 0.0070 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 282 HIS B 240 GLN B 277 ASN B 282 HIS C 122 ASN C 240 GLN ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6669 Z= 0.214 Angle : 0.691 7.706 9084 Z= 0.368 Chirality : 0.047 0.230 957 Planarity : 0.006 0.073 1188 Dihedral : 9.776 92.592 937 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.26 % Favored : 93.50 % Rotamer: Outliers : 4.37 % Allowed : 13.83 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % 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: -2.97 (0.26), residues: 831 helix: -3.14 (0.38), residues: 117 sheet: -0.70 (0.50), residues: 90 loop : -2.10 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.009 0.002 HIS B 255 PHE 0.012 0.001 PHE B 259 TYR 0.025 0.002 TYR A 208 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8423 (ptmm) cc_final: 0.8048 (ttmt) REVERT: A 293 GLU cc_start: 0.6522 (tt0) cc_final: 0.6107 (tt0) REVERT: A 298 GLN cc_start: 0.8122 (mt0) cc_final: 0.7868 (mt0) REVERT: B 79 GLN cc_start: 0.8947 (tt0) cc_final: 0.8608 (tt0) REVERT: B 158 ASP cc_start: 0.7284 (t0) cc_final: 0.6519 (t0) REVERT: B 212 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 234 THR cc_start: 0.7094 (m) cc_final: 0.6827 (p) REVERT: B 307 TRP cc_start: 0.7080 (t-100) cc_final: 0.6605 (t-100) REVERT: B 310 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8393 (mt) REVERT: C 163 ASP cc_start: 0.6467 (m-30) cc_final: 0.6254 (m-30) REVERT: C 202 PHE cc_start: 0.8053 (m-80) cc_final: 0.7825 (m-80) REVERT: C 231 PHE cc_start: 0.7978 (t80) cc_final: 0.7747 (t80) outliers start: 30 outliers final: 14 residues processed: 145 average time/residue: 0.2045 time to fit residues: 38.1426 Evaluate side-chains 113 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN C 255 HIS C 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6669 Z= 0.320 Angle : 0.704 7.313 9084 Z= 0.378 Chirality : 0.050 0.196 957 Planarity : 0.006 0.080 1188 Dihedral : 8.723 58.562 921 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.95 % Allowed : 15.72 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % Twisted General : 0.75 % 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: -2.83 (0.27), residues: 831 helix: -2.80 (0.37), residues: 135 sheet: -0.44 (0.44), residues: 120 loop : -2.10 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 94 HIS 0.006 0.001 HIS B 255 PHE 0.016 0.002 PHE B 330 TYR 0.018 0.002 TYR A 204 ARG 0.005 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8474 (ptmm) REVERT: A 272 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8495 (pp) REVERT: A 293 GLU cc_start: 0.6871 (tt0) cc_final: 0.6497 (tt0) REVERT: B 202 PHE cc_start: 0.8148 (m-10) cc_final: 0.7938 (m-10) REVERT: C 202 PHE cc_start: 0.8375 (m-80) cc_final: 0.8115 (m-80) REVERT: C 261 ASN cc_start: 0.7833 (m-40) cc_final: 0.7619 (m-40) REVERT: C 272 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8800 (pp) outliers start: 34 outliers final: 19 residues processed: 133 average time/residue: 0.2485 time to fit residues: 41.0352 Evaluate side-chains 118 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 293 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 78 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 298 GLN B 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 6669 Z= 0.462 Angle : 0.781 7.694 9084 Z= 0.415 Chirality : 0.053 0.192 957 Planarity : 0.007 0.087 1188 Dihedral : 8.795 58.529 920 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.90 % Favored : 90.97 % Rotamer: Outliers : 6.11 % Allowed : 15.57 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % Twisted General : 0.75 % 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: -2.63 (0.27), residues: 831 helix: -2.47 (0.42), residues: 117 sheet: -0.59 (0.43), residues: 120 loop : -1.97 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 307 HIS 0.006 0.002 HIS B 187 PHE 0.020 0.002 PHE A 330 TYR 0.020 0.003 TYR B 151 ARG 0.007 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 102 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7629 (m-30) cc_final: 0.7370 (m-30) REVERT: A 191 GLU cc_start: 0.7801 (mp0) cc_final: 0.7548 (mp0) REVERT: A 272 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8696 (pp) REVERT: B 73 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8327 (mt) REVERT: B 212 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8479 (t80) REVERT: C 62 LYS cc_start: 0.8206 (tptp) cc_final: 0.8002 (tptp) REVERT: C 202 PHE cc_start: 0.8566 (m-80) cc_final: 0.8327 (m-80) REVERT: C 208 TYR cc_start: 0.5270 (t80) cc_final: 0.4665 (t80) REVERT: C 272 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (pp) REVERT: C 275 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7827 (mt) outliers start: 42 outliers final: 23 residues processed: 133 average time/residue: 0.2759 time to fit residues: 44.6363 Evaluate side-chains 118 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6669 Z= 0.346 Angle : 0.723 9.659 9084 Z= 0.385 Chirality : 0.050 0.194 957 Planarity : 0.006 0.081 1188 Dihedral : 8.265 59.037 914 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.30 % Favored : 91.58 % Rotamer: Outliers : 5.24 % Allowed : 16.74 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.28), residues: 831 helix: -2.48 (0.42), residues: 114 sheet: -0.58 (0.44), residues: 120 loop : -1.89 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.016 0.002 PHE B 330 TYR 0.015 0.002 TYR B 151 ARG 0.009 0.001 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7743 (m-30) cc_final: 0.7530 (m-30) REVERT: A 163 ASP cc_start: 0.8109 (m-30) cc_final: 0.7764 (m-30) REVERT: A 177 GLN cc_start: 0.8185 (mp10) cc_final: 0.7944 (mt0) REVERT: A 293 GLU cc_start: 0.7157 (tt0) cc_final: 0.6761 (tt0) REVERT: B 212 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8390 (t80) REVERT: B 310 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8436 (mt) REVERT: C 87 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7542 (mpp) REVERT: C 202 PHE cc_start: 0.8409 (m-80) cc_final: 0.8152 (m-80) REVERT: C 208 TYR cc_start: 0.5112 (t80) cc_final: 0.4721 (t80) REVERT: C 272 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8700 (pp) outliers start: 36 outliers final: 22 residues processed: 122 average time/residue: 0.2641 time to fit residues: 39.5271 Evaluate side-chains 120 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 41 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6669 Z= 0.325 Angle : 0.724 12.957 9084 Z= 0.384 Chirality : 0.049 0.194 957 Planarity : 0.007 0.081 1188 Dihedral : 8.185 58.374 914 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.18 % Favored : 91.46 % Rotamer: Outliers : 5.53 % Allowed : 16.59 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % Twisted General : 0.75 % 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: -2.36 (0.28), residues: 831 helix: -2.27 (0.47), residues: 96 sheet: -0.57 (0.53), residues: 87 loop : -1.74 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.015 0.001 PHE B 330 TYR 0.012 0.002 TYR C 212 ARG 0.006 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 101 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7836 (p0) cc_final: 0.7612 (p0) REVERT: A 131 ASP cc_start: 0.7634 (m-30) cc_final: 0.7357 (m-30) REVERT: A 132 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7522 (mtm-85) REVERT: A 163 ASP cc_start: 0.8055 (m-30) cc_final: 0.7831 (m-30) REVERT: A 177 GLN cc_start: 0.8212 (mp10) cc_final: 0.8004 (mt0) REVERT: A 293 GLU cc_start: 0.7266 (tt0) cc_final: 0.6844 (tt0) REVERT: B 73 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8208 (mt) REVERT: B 212 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 310 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8402 (mt) REVERT: C 87 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7530 (mpp) REVERT: C 202 PHE cc_start: 0.8428 (m-80) cc_final: 0.8149 (m-80) REVERT: C 208 TYR cc_start: 0.4864 (t80) cc_final: 0.4536 (t80) REVERT: C 272 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8645 (pp) REVERT: C 275 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7875 (mt) outliers start: 38 outliers final: 28 residues processed: 125 average time/residue: 0.2494 time to fit residues: 38.6139 Evaluate side-chains 122 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6669 Z= 0.304 Angle : 0.711 9.496 9084 Z= 0.379 Chirality : 0.049 0.195 957 Planarity : 0.006 0.079 1188 Dihedral : 8.124 57.976 914 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.90 % Favored : 90.85 % Rotamer: Outliers : 5.97 % Allowed : 16.59 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % Twisted General : 0.88 % 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 (0.28), residues: 831 helix: -2.16 (0.47), residues: 96 sheet: -0.53 (0.54), residues: 87 loop : -1.68 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.015 0.001 PHE B 184 TYR 0.027 0.002 TYR B 208 ARG 0.005 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 100 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7688 (p0) cc_final: 0.7455 (p0) REVERT: A 131 ASP cc_start: 0.7641 (m-30) cc_final: 0.7361 (m-30) REVERT: A 132 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7327 (mtm-85) REVERT: A 177 GLN cc_start: 0.8191 (mp10) cc_final: 0.7792 (mt0) REVERT: A 293 GLU cc_start: 0.7273 (tt0) cc_final: 0.6847 (tt0) REVERT: B 73 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8210 (mt) REVERT: B 212 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8378 (t80) REVERT: C 87 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7514 (mpp) REVERT: C 202 PHE cc_start: 0.8412 (m-80) cc_final: 0.8146 (m-80) REVERT: C 207 PHE cc_start: 0.4323 (OUTLIER) cc_final: 0.3911 (p90) REVERT: C 208 TYR cc_start: 0.4691 (t80) cc_final: 0.4378 (t80) REVERT: C 272 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8617 (pp) REVERT: C 275 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7960 (mt) outliers start: 41 outliers final: 30 residues processed: 128 average time/residue: 0.2477 time to fit residues: 39.4936 Evaluate side-chains 127 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 91 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6669 Z= 0.235 Angle : 0.684 9.991 9084 Z= 0.363 Chirality : 0.047 0.222 957 Planarity : 0.006 0.077 1188 Dihedral : 7.876 56.542 914 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.06 % Favored : 91.70 % Rotamer: Outliers : 5.82 % Allowed : 18.05 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.88 % 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: -2.17 (0.28), residues: 831 helix: -1.91 (0.49), residues: 96 sheet: -0.44 (0.55), residues: 87 loop : -1.64 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 134 HIS 0.004 0.001 HIS B 255 PHE 0.011 0.001 PHE B 184 TYR 0.039 0.002 TYR B 208 ARG 0.005 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 102 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7603 (m-30) cc_final: 0.7307 (m-30) REVERT: A 293 GLU cc_start: 0.7107 (tt0) cc_final: 0.6567 (tt0) REVERT: B 73 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8166 (mt) REVERT: B 212 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8460 (t80) REVERT: B 310 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8413 (mt) REVERT: C 87 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7636 (mpp) REVERT: C 202 PHE cc_start: 0.8363 (m-80) cc_final: 0.8155 (m-80) REVERT: C 207 PHE cc_start: 0.4413 (OUTLIER) cc_final: 0.4033 (p90) REVERT: C 208 TYR cc_start: 0.4380 (t80) cc_final: 0.4094 (t80) REVERT: C 272 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8635 (pp) REVERT: C 275 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7685 (mt) outliers start: 40 outliers final: 23 residues processed: 128 average time/residue: 0.2843 time to fit residues: 45.0515 Evaluate side-chains 122 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6669 Z= 0.332 Angle : 0.742 10.285 9084 Z= 0.394 Chirality : 0.050 0.200 957 Planarity : 0.006 0.081 1188 Dihedral : 8.003 58.590 914 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.51 % Favored : 90.25 % Rotamer: Outliers : 5.24 % Allowed : 19.36 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % Twisted General : 0.75 % 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: -2.26 (0.28), residues: 831 helix: -2.07 (0.48), residues: 96 sheet: -0.53 (0.55), residues: 87 loop : -1.68 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.005 0.001 HIS B 187 PHE 0.016 0.002 PHE B 330 TYR 0.018 0.002 TYR B 208 ARG 0.006 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7707 (p0) cc_final: 0.7148 (p0) REVERT: A 131 ASP cc_start: 0.7695 (m-30) cc_final: 0.7445 (m-30) REVERT: A 132 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7444 (mtm-85) REVERT: A 293 GLU cc_start: 0.7241 (tt0) cc_final: 0.6858 (tt0) REVERT: B 73 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 212 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 310 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8443 (mt) REVERT: C 87 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7463 (mpp) REVERT: C 202 PHE cc_start: 0.8423 (m-80) cc_final: 0.8127 (m-80) REVERT: C 207 PHE cc_start: 0.4313 (OUTLIER) cc_final: 0.3895 (p90) REVERT: C 272 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8575 (pp) REVERT: C 275 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7870 (mt) outliers start: 36 outliers final: 27 residues processed: 122 average time/residue: 0.2626 time to fit residues: 39.2770 Evaluate side-chains 128 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.0030 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6669 Z= 0.285 Angle : 0.715 9.550 9084 Z= 0.381 Chirality : 0.048 0.210 957 Planarity : 0.006 0.077 1188 Dihedral : 7.834 57.508 914 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.54 % Favored : 91.34 % Rotamer: Outliers : 5.39 % Allowed : 19.07 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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: -2.17 (0.28), residues: 831 helix: -1.99 (0.49), residues: 96 sheet: -0.48 (0.55), residues: 87 loop : -1.61 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 307 HIS 0.005 0.001 HIS A 255 PHE 0.013 0.001 PHE B 330 TYR 0.026 0.002 TYR C 208 ARG 0.005 0.001 ARG B 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7671 (p0) cc_final: 0.7114 (p0) REVERT: A 131 ASP cc_start: 0.7686 (m-30) cc_final: 0.7439 (m-30) REVERT: A 132 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7404 (mtm-85) REVERT: A 293 GLU cc_start: 0.7238 (tt0) cc_final: 0.6805 (tt0) REVERT: B 73 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8245 (mt) REVERT: B 212 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8241 (t80) REVERT: B 310 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8429 (mt) REVERT: C 87 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7457 (mpp) REVERT: C 202 PHE cc_start: 0.8359 (m-80) cc_final: 0.8141 (m-80) REVERT: C 272 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8582 (pp) REVERT: C 275 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7862 (mt) outliers start: 37 outliers final: 28 residues processed: 119 average time/residue: 0.2494 time to fit residues: 36.9692 Evaluate side-chains 127 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 293 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107887 restraints weight = 9835.098| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.80 r_work: 0.3221 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6669 Z= 0.244 Angle : 0.694 8.899 9084 Z= 0.369 Chirality : 0.047 0.215 957 Planarity : 0.006 0.076 1188 Dihedral : 7.630 56.142 914 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.18 % Favored : 91.70 % Rotamer: Outliers : 5.09 % Allowed : 19.51 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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: -2.08 (0.29), residues: 831 helix: -1.88 (0.49), residues: 96 sheet: -0.45 (0.55), residues: 87 loop : -1.56 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 307 HIS 0.005 0.001 HIS A 255 PHE 0.015 0.001 PHE B 184 TYR 0.024 0.002 TYR C 208 ARG 0.004 0.000 ARG B 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1699.04 seconds wall clock time: 30 minutes 48.51 seconds (1848.51 seconds total)