Starting phenix.real_space_refine on Thu Mar 14 23:24:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/03_2024/8g15_29662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/03_2024/8g15_29662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/03_2024/8g15_29662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/03_2024/8g15_29662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/03_2024/8g15_29662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g15_29662/03_2024/8g15_29662.pdb" } resolution = 2.07 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6352 2.51 5 N 1744 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D ARG 234": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.10, per 1000 atoms: 0.51 Number of scatterers: 10056 At special positions: 0 Unit cell: (99.365, 102.705, 89.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1912 8.00 N 1744 7.00 C 6352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.55 Conformation dependent library (CDL) restraints added in 1.9 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 38.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.565A pdb=" N ILE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.832A pdb=" N GLN A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.517A pdb=" N ASN A 287 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 334 removed outlier: 3.519A pdb=" N VAL A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.566A pdb=" N ILE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.833A pdb=" N GLN B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR B 140 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.517A pdb=" N ASN B 287 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 334 removed outlier: 3.518A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.564A pdb=" N ILE C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.831A pdb=" N GLN C 113 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR C 140 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.516A pdb=" N ASN C 287 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 removed outlier: 3.516A pdb=" N VAL C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.565A pdb=" N ILE D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.900A pdb=" N GLN D 113 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.521A pdb=" N TYR D 140 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.518A pdb=" N ASN D 287 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 334 removed outlier: 3.518A pdb=" N VAL D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 5.941A pdb=" N VAL A 31 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.571A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 172 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 12.260A pdb=" N PHE A 307 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY A 300 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N LYS A 309 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N GLY A 298 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.938A pdb=" N VAL B 31 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 6 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 32 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.531A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 172 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 12.258A pdb=" N PHE B 307 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY B 300 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N LYS B 309 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLY B 298 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63 removed outlier: 5.939A pdb=" N VAL C 31 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 6 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 32 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.585A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 172 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 12.256A pdb=" N PHE C 307 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N GLY C 300 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N LYS C 309 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLY C 298 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.941A pdb=" N VAL D 31 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.586A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D 172 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 12.257A pdb=" N PHE D 307 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY D 300 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N LYS D 309 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLY D 298 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 3.84 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: 3109 1.34 - 1.45: 1446 1.45 - 1.57: 5617 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10256 Sorted by residual: bond pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 1.329 1.482 -0.152 1.38e-02 5.25e+03 1.22e+02 bond pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 1.329 1.477 -0.148 1.38e-02 5.25e+03 1.15e+02 bond pdb=" C SER C 312 " pdb=" N TRP C 313 " ideal model delta sigma weight residual 1.329 1.475 -0.146 1.38e-02 5.25e+03 1.12e+02 bond pdb=" N PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.42e+01 bond pdb=" N VAL D 188 " pdb=" CA VAL D 188 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.60e+00 ... (remaining 10251 not shown) Histogram of bond angle deviations from ideal: 94.94 - 102.92: 72 102.92 - 110.91: 3656 110.91 - 118.90: 4721 118.90 - 126.89: 5331 126.89 - 134.88: 116 Bond angle restraints: 13896 Sorted by residual: angle pdb=" O SER B 312 " pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 123.24 94.94 28.30 1.23e+00 6.61e-01 5.30e+02 angle pdb=" O SER D 312 " pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 123.24 94.94 28.30 1.23e+00 6.61e-01 5.29e+02 angle pdb=" O SER C 312 " pdb=" C SER C 312 " pdb=" N TRP C 313 " ideal model delta sigma weight residual 123.24 95.09 28.15 1.23e+00 6.61e-01 5.24e+02 angle pdb=" CA SER D 312 " pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 115.58 134.88 -19.30 1.48e+00 4.57e-01 1.70e+02 angle pdb=" CA SER B 312 " pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 115.58 134.81 -19.23 1.48e+00 4.57e-01 1.69e+02 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 5348 17.21 - 34.42: 514 34.42 - 51.63: 147 51.63 - 68.84: 53 68.84 - 86.05: 13 Dihedral angle restraints: 6075 sinusoidal: 2299 harmonic: 3776 Sorted by residual: dihedral pdb=" CA ASN B 239 " pdb=" C ASN B 239 " pdb=" N VAL B 240 " pdb=" CA VAL B 240 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN D 239 " pdb=" C ASN D 239 " pdb=" N VAL D 240 " pdb=" CA VAL D 240 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN C 239 " pdb=" C ASN C 239 " pdb=" N VAL C 240 " pdb=" CA VAL C 240 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 968 0.040 - 0.080: 381 0.080 - 0.120: 172 0.120 - 0.160: 46 0.160 - 0.200: 9 Chirality restraints: 1576 Sorted by residual: chirality pdb=" CA ILE C 207 " pdb=" N ILE C 207 " pdb=" C ILE C 207 " pdb=" CB ILE C 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE D 207 " pdb=" N ILE D 207 " pdb=" C ILE D 207 " pdb=" CB ILE D 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 1573 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 312 " -0.069 2.00e-02 2.50e+03 1.08e-01 1.16e+02 pdb=" C SER C 312 " 0.187 2.00e-02 2.50e+03 pdb=" O SER C 312 " -0.058 2.00e-02 2.50e+03 pdb=" N TRP C 313 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 312 " 0.068 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C SER B 312 " -0.183 2.00e-02 2.50e+03 pdb=" O SER B 312 " 0.057 2.00e-02 2.50e+03 pdb=" N TRP B 313 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 312 " -0.068 2.00e-02 2.50e+03 1.06e-01 1.11e+02 pdb=" C SER D 312 " 0.183 2.00e-02 2.50e+03 pdb=" O SER D 312 " -0.056 2.00e-02 2.50e+03 pdb=" N TRP D 313 " -0.058 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1932 2.77 - 3.31: 8802 3.31 - 3.84: 16550 3.84 - 4.37: 20098 4.37 - 4.90: 35079 Nonbonded interactions: 82461 Sorted by model distance: nonbonded pdb=" O ASN B 239 " pdb=" OD1 ASN B 316 " model vdw 2.243 3.040 nonbonded pdb=" O ASN D 239 " pdb=" OD1 ASN D 316 " model vdw 2.243 3.040 nonbonded pdb=" O ASN C 239 " pdb=" OD1 ASN C 316 " model vdw 2.251 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OD1 ASN A 316 " model vdw 2.255 3.040 nonbonded pdb=" NH2 ARG C 118 " pdb=" OD1 ASN C 142 " model vdw 2.257 2.520 ... (remaining 82456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.180 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: 3.470 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.730 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 : 0.005 0.152 10256 Z= 0.364 Angle : 0.963 28.304 13896 Z= 0.638 Chirality : 0.054 0.200 1576 Planarity : 0.009 0.120 1804 Dihedral : 16.072 86.054 3667 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.59 % Allowed : 16.21 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.22), residues: 1328 helix: -2.29 (0.18), residues: 388 sheet: 0.29 (0.40), residues: 220 loop : -0.71 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 87 HIS 0.003 0.001 HIS B 53 PHE 0.009 0.001 PHE B 233 TYR 0.010 0.002 TYR D 42 ARG 0.021 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.179 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 104 average time/residue: 1.4222 time to fit residues: 157.6474 Evaluate side-chains 97 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.1980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 149 ASN C 149 ASN D 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10256 Z= 0.201 Angle : 0.537 5.951 13896 Z= 0.297 Chirality : 0.046 0.150 1576 Planarity : 0.005 0.052 1804 Dihedral : 5.732 40.622 1431 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.00 % Allowed : 15.09 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1328 helix: -0.04 (0.24), residues: 392 sheet: 0.54 (0.40), residues: 212 loop : -0.56 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.002 0.000 HIS D 53 PHE 0.007 0.001 PHE D 286 TYR 0.011 0.001 TYR D 314 ARG 0.008 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 1.021 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 101 average time/residue: 1.4106 time to fit residues: 151.9751 Evaluate side-chains 90 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8965 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 10256 Z= 0.442 Angle : 0.668 9.054 13896 Z= 0.368 Chirality : 0.053 0.153 1576 Planarity : 0.006 0.055 1804 Dihedral : 6.604 54.650 1423 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.91 % Allowed : 15.93 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1328 helix: 0.55 (0.25), residues: 376 sheet: 0.48 (0.39), residues: 204 loop : -0.59 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 87 HIS 0.003 0.001 HIS A 53 PHE 0.012 0.002 PHE A 318 TYR 0.017 0.002 TYR B 314 ARG 0.006 0.001 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.113 Fit side-chains outliers start: 31 outliers final: 24 residues processed: 99 average time/residue: 1.4101 time to fit residues: 148.9984 Evaluate side-chains 95 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8905 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10256 Z= 0.161 Angle : 0.510 6.638 13896 Z= 0.279 Chirality : 0.046 0.136 1576 Planarity : 0.005 0.052 1804 Dihedral : 5.903 53.187 1423 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.00 % Allowed : 16.31 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1328 helix: 0.80 (0.26), residues: 396 sheet: 0.49 (0.39), residues: 212 loop : -0.41 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 87 HIS 0.002 0.001 HIS D 179 PHE 0.005 0.001 PHE D 286 TYR 0.009 0.001 TYR D 314 ARG 0.008 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 1.227 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 104 average time/residue: 1.4444 time to fit residues: 160.3621 Evaluate side-chains 93 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10256 Z= 0.248 Angle : 0.564 7.678 13896 Z= 0.310 Chirality : 0.048 0.143 1576 Planarity : 0.005 0.060 1804 Dihedral : 6.180 57.357 1423 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.03 % Allowed : 15.18 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1328 helix: 1.11 (0.27), residues: 376 sheet: 0.51 (0.39), residues: 204 loop : -0.47 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 87 HIS 0.002 0.001 HIS D 53 PHE 0.007 0.001 PHE C 286 TYR 0.012 0.001 TYR C 314 ARG 0.009 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 78 time to evaluate : 1.218 Fit side-chains outliers start: 43 outliers final: 34 residues processed: 115 average time/residue: 1.2517 time to fit residues: 154.7327 Evaluate side-chains 104 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 70 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8920 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10256 Z= 0.201 Angle : 0.541 7.202 13896 Z= 0.295 Chirality : 0.047 0.137 1576 Planarity : 0.005 0.061 1804 Dihedral : 6.095 59.500 1423 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.47 % Allowed : 15.65 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1328 helix: 1.17 (0.27), residues: 380 sheet: 0.47 (0.39), residues: 212 loop : -0.40 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 87 HIS 0.002 0.001 HIS D 137 PHE 0.006 0.001 PHE B 286 TYR 0.011 0.001 TYR C 314 ARG 0.015 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 1.160 Fit side-chains outliers start: 37 outliers final: 31 residues processed: 109 average time/residue: 1.2544 time to fit residues: 147.0656 Evaluate side-chains 105 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.8907 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10256 Z= 0.169 Angle : 0.508 6.642 13896 Z= 0.277 Chirality : 0.046 0.136 1576 Planarity : 0.005 0.068 1804 Dihedral : 5.805 58.094 1420 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.84 % Allowed : 15.84 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1328 helix: 1.27 (0.27), residues: 380 sheet: 0.49 (0.39), residues: 212 loop : -0.40 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS A 137 PHE 0.005 0.001 PHE D 286 TYR 0.010 0.001 TYR B 314 ARG 0.017 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 78 time to evaluate : 1.148 Fit side-chains REVERT: A 39 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7689 (p0) REVERT: B 39 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7659 (p0) REVERT: C 39 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7649 (p0) outliers start: 41 outliers final: 30 residues processed: 114 average time/residue: 1.2711 time to fit residues: 155.9105 Evaluate side-chains 108 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 75 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.0370 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10256 Z= 0.216 Angle : 0.559 7.172 13896 Z= 0.306 Chirality : 0.047 0.139 1576 Planarity : 0.006 0.071 1804 Dihedral : 5.797 54.516 1419 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.09 % Allowed : 16.96 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1328 helix: 1.18 (0.27), residues: 380 sheet: 0.51 (0.39), residues: 204 loop : -0.51 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 87 HIS 0.002 0.001 HIS A 53 PHE 0.006 0.001 PHE A 286 TYR 0.012 0.001 TYR D 314 ARG 0.017 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 1.220 Fit side-chains outliers start: 33 outliers final: 28 residues processed: 105 average time/residue: 1.3537 time to fit residues: 152.3069 Evaluate side-chains 103 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 264 GLN B 264 GLN C 149 ASN D 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10256 Z= 0.141 Angle : 0.494 6.459 13896 Z= 0.268 Chirality : 0.045 0.133 1576 Planarity : 0.005 0.077 1804 Dihedral : 5.486 52.443 1419 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.53 % Allowed : 16.87 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1328 helix: 1.18 (0.27), residues: 396 sheet: 0.56 (0.39), residues: 212 loop : -0.40 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.000 HIS D 137 PHE 0.005 0.001 PHE A 77 TYR 0.008 0.001 TYR D 314 ARG 0.018 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 1.201 Fit side-chains outliers start: 27 outliers final: 26 residues processed: 98 average time/residue: 1.3151 time to fit residues: 138.2126 Evaluate side-chains 101 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 10 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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: 0.8918 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10256 Z= 0.210 Angle : 0.561 6.933 13896 Z= 0.306 Chirality : 0.047 0.139 1576 Planarity : 0.006 0.079 1804 Dihedral : 5.658 51.534 1419 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.72 % Allowed : 16.87 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1328 helix: 1.23 (0.27), residues: 380 sheet: 0.50 (0.39), residues: 212 loop : -0.48 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 87 HIS 0.002 0.001 HIS D 53 PHE 0.006 0.001 PHE B 286 TYR 0.011 0.001 TYR C 314 ARG 0.019 0.001 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.199 Fit side-chains outliers start: 29 outliers final: 25 residues processed: 96 average time/residue: 1.2656 time to fit residues: 130.8581 Evaluate side-chains 97 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN D 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083743 restraints weight = 16812.336| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.92 r_work: 0.3215 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10256 Z= 0.142 Angle : 0.494 6.926 13896 Z= 0.267 Chirality : 0.045 0.133 1576 Planarity : 0.006 0.080 1804 Dihedral : 5.399 49.834 1419 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.34 % Allowed : 17.15 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1328 helix: 1.15 (0.27), residues: 396 sheet: 0.57 (0.39), residues: 212 loop : -0.37 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.000 HIS B 137 PHE 0.005 0.001 PHE A 77 TYR 0.008 0.001 TYR C 314 ARG 0.019 0.001 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.38 seconds wall clock time: 61 minutes 20.90 seconds (3680.90 seconds total)