Starting phenix.real_space_refine on Wed Feb 14 03:08:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2024/7y12_33554_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2024/7y12_33554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2024/7y12_33554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2024/7y12_33554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2024/7y12_33554_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y12_33554/02_2024/7y12_33554_updated.pdb" } resolution = 3.1 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= 0.002 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 69 5.16 5 C 5431 2.51 5 N 1454 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 275": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8501 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1654 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2053 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'BAL': 1, 'PLM': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.95, per 1000 atoms: 0.58 Number of scatterers: 8501 At special positions: 0 Unit cell: (122.85, 84.375, 124.2, 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 69 16.00 O 1547 8.00 N 1454 7.00 C 5431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 2082 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 33.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.807A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.075A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.887A pdb=" N VAL A 335 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'R' and resid 23 through 51 Processing helix chain 'R' and resid 63 through 87 Processing helix chain 'R' and resid 93 through 128 removed outlier: 3.985A pdb=" N VAL R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 141 through 162 Processing helix chain 'R' and resid 172 through 208 removed outlier: 5.168A pdb=" N THR R 191 " --> pdb=" O MET R 187 " (cutoff:3.500A) Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 217 through 233 Processing helix chain 'R' and resid 235 through 246 removed outlier: 5.040A pdb=" N TYR R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP R 246 " --> pdb=" O PHE R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 276 Proline residue: R 273 - end of helix Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.173A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.868A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.034A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.690A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.701A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.401A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.958A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.596A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.764A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= L, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.508A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1083 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: 2.22 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2292 1.33 - 1.45: 1585 1.45 - 1.57: 4699 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8676 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.306 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.508 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.511 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.512 0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C LEU R 235 " pdb=" N PRO R 236 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.00e+00 ... (remaining 8671 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.65: 197 106.65 - 113.48: 4837 113.48 - 120.31: 3002 120.31 - 127.14: 3624 127.14 - 133.98: 96 Bond angle restraints: 11756 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.33 7.47 1.70e+00 3.46e-01 1.93e+01 angle pdb=" CB MET R 42 " pdb=" CG MET R 42 " pdb=" SD MET R 42 " ideal model delta sigma weight residual 112.70 123.74 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA MET R 42 " pdb=" CB MET R 42 " pdb=" CG MET R 42 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.25e+00 angle pdb=" N MET R 42 " pdb=" CA MET R 42 " pdb=" CB MET R 42 " ideal model delta sigma weight residual 110.30 114.67 -4.37 1.54e+00 4.22e-01 8.03e+00 ... (remaining 11751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4517 17.97 - 35.93: 479 35.93 - 53.90: 110 53.90 - 71.86: 13 71.86 - 89.83: 12 Dihedral angle restraints: 5131 sinusoidal: 1912 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 63.90 29.10 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA ASP B 303 " pdb=" CB ASP B 303 " pdb=" CG ASP B 303 " pdb=" OD1 ASP B 303 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 808 0.028 - 0.056: 355 0.056 - 0.085: 112 0.085 - 0.113: 67 0.113 - 0.141: 15 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1354 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.010 2.00e-02 2.50e+03 9.66e-03 1.87e+00 pdb=" CG TYR B 105 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO B 236 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 240 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C TYR R 240 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR R 240 " -0.008 2.00e-02 2.50e+03 pdb=" N TRP R 241 " -0.008 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 131 2.65 - 3.21: 7668 3.21 - 3.77: 13416 3.77 - 4.34: 18426 4.34 - 4.90: 30789 Nonbonded interactions: 70430 Sorted by model distance: nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.086 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.147 2.440 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.187 2.520 nonbonded pdb=" OD1 ASN A 241 " pdb=" OH TYR A 287 " model vdw 2.213 2.440 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.262 2.440 ... (remaining 70425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.430 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: 0.000 Extract box with map and model: 6.790 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.850 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.003 0.059 8676 Z= 0.222 Angle : 0.581 11.036 11756 Z= 0.295 Chirality : 0.040 0.141 1357 Planarity : 0.003 0.033 1468 Dihedral : 15.813 89.828 3043 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.22 % Allowed : 15.96 % Favored : 83.82 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.86 (0.27), residues: 1093 helix: 2.18 (0.28), residues: 361 sheet: -0.05 (0.32), residues: 271 loop : -0.27 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE R 75 TYR 0.024 0.002 TYR B 105 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.965 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.2105 time to fit residues: 41.8563 Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.0040 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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: 0.7637 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8676 Z= 0.133 Angle : 0.467 5.444 11756 Z= 0.252 Chirality : 0.039 0.144 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.312 49.993 1242 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.91 % Allowed : 15.51 % Favored : 82.58 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 1.04 (0.27), residues: 1093 helix: 2.33 (0.28), residues: 371 sheet: -0.01 (0.32), residues: 271 loop : -0.17 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE R 75 TYR 0.010 0.001 TYR S 60 ARG 0.002 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.073 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 163 average time/residue: 0.1995 time to fit residues: 45.1513 Evaluate side-chains 155 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8676 Z= 0.268 Angle : 0.545 6.939 11756 Z= 0.291 Chirality : 0.042 0.152 1357 Planarity : 0.004 0.033 1468 Dihedral : 5.919 56.302 1239 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.81 % Allowed : 17.98 % Favored : 79.21 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.70 (0.26), residues: 1093 helix: 2.04 (0.28), residues: 356 sheet: -0.12 (0.31), residues: 287 loop : -0.34 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 144 HIS 0.004 0.001 HIS S 35 PHE 0.022 0.002 PHE R 75 TYR 0.020 0.002 TYR B 105 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.965 Fit side-chains REVERT: A 5 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7418 (mp) REVERT: B 105 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7430 (t80) REVERT: R 95 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5916 (t70) outliers start: 25 outliers final: 15 residues processed: 154 average time/residue: 0.2018 time to fit residues: 43.2399 Evaluate side-chains 157 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8676 Z= 0.326 Angle : 0.589 5.791 11756 Z= 0.315 Chirality : 0.043 0.168 1357 Planarity : 0.004 0.033 1468 Dihedral : 6.498 58.485 1239 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.93 % Allowed : 19.55 % Favored : 76.52 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.35 (0.26), residues: 1093 helix: 1.68 (0.28), residues: 353 sheet: -0.22 (0.30), residues: 287 loop : -0.54 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 144 HIS 0.004 0.001 HIS B 142 PHE 0.022 0.002 PHE R 75 TYR 0.023 0.002 TYR B 105 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.043 Fit side-chains REVERT: A 5 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7492 (mp) REVERT: B 105 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7623 (t80) REVERT: B 340 ASN cc_start: 0.8042 (t0) cc_final: 0.7735 (t0) REVERT: R 95 ASP cc_start: 0.6193 (OUTLIER) cc_final: 0.5874 (t70) outliers start: 35 outliers final: 24 residues processed: 159 average time/residue: 0.2114 time to fit residues: 46.8350 Evaluate side-chains 158 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7701 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.178 Angle : 0.494 5.212 11756 Z= 0.265 Chirality : 0.040 0.146 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.706 59.143 1239 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.37 % Allowed : 20.22 % Favored : 76.40 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.64 (0.26), residues: 1093 helix: 2.01 (0.28), residues: 355 sheet: -0.16 (0.31), residues: 276 loop : -0.39 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE A 334 TYR 0.015 0.001 TYR B 105 ARG 0.002 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 0.999 Fit side-chains outliers start: 30 outliers final: 23 residues processed: 165 average time/residue: 0.2022 time to fit residues: 46.0790 Evaluate side-chains 161 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7691 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.171 Angle : 0.488 5.225 11756 Z= 0.260 Chirality : 0.039 0.145 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.397 57.314 1239 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.82 % Allowed : 20.45 % Favored : 75.73 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.76 (0.26), residues: 1093 helix: 2.10 (0.28), residues: 362 sheet: -0.12 (0.31), residues: 275 loop : -0.32 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE R 75 TYR 0.013 0.001 TYR B 105 ARG 0.003 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 0.940 Fit side-chains REVERT: A 5 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7380 (mp) REVERT: B 105 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7317 (t80) REVERT: R 79 MET cc_start: 0.6938 (tpp) cc_final: 0.6645 (tpp) REVERT: R 156 MET cc_start: 0.7759 (mmm) cc_final: 0.7506 (mmt) outliers start: 34 outliers final: 25 residues processed: 166 average time/residue: 0.1996 time to fit residues: 45.6427 Evaluate side-chains 165 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8676 Z= 0.162 Angle : 0.483 5.264 11756 Z= 0.258 Chirality : 0.039 0.146 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.249 56.795 1239 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.04 % Allowed : 20.67 % Favored : 75.28 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.87 (0.26), residues: 1093 helix: 2.20 (0.28), residues: 367 sheet: -0.08 (0.31), residues: 275 loop : -0.28 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.022 0.001 PHE A 334 TYR 0.012 0.001 TYR B 105 ARG 0.004 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 0.974 Fit side-chains REVERT: A 5 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7373 (mp) REVERT: R 51 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6586 (mp) REVERT: R 156 MET cc_start: 0.7756 (mmm) cc_final: 0.7526 (mmt) REVERT: S 113 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6333 (mm-40) outliers start: 36 outliers final: 28 residues processed: 169 average time/residue: 0.2051 time to fit residues: 47.6991 Evaluate side-chains 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7731 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8676 Z= 0.254 Angle : 0.545 8.439 11756 Z= 0.287 Chirality : 0.041 0.157 1357 Planarity : 0.004 0.032 1468 Dihedral : 5.867 57.192 1239 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.49 % Allowed : 20.56 % Favored : 74.94 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.60 (0.26), residues: 1093 helix: 2.01 (0.28), residues: 354 sheet: -0.17 (0.31), residues: 278 loop : -0.45 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 144 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.002 PHE R 75 TYR 0.018 0.002 TYR B 105 ARG 0.004 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 0.952 Fit side-chains REVERT: A 5 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7465 (mp) REVERT: B 105 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7557 (t80) REVERT: B 142 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.6571 (m170) outliers start: 40 outliers final: 32 residues processed: 173 average time/residue: 0.2003 time to fit residues: 47.8096 Evaluate side-chains 178 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.7666 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8676 Z= 0.144 Angle : 0.484 7.641 11756 Z= 0.254 Chirality : 0.039 0.145 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.174 55.260 1239 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.48 % Allowed : 21.91 % Favored : 74.61 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.90 (0.27), residues: 1093 helix: 2.24 (0.28), residues: 367 sheet: -0.07 (0.32), residues: 275 loop : -0.28 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.003 0.000 HIS S 35 PHE 0.022 0.001 PHE A 334 TYR 0.010 0.001 TYR B 105 ARG 0.003 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 0.935 Fit side-chains REVERT: A 5 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7373 (mp) REVERT: A 52 GLN cc_start: 0.5868 (OUTLIER) cc_final: 0.5203 (pp30) REVERT: B 105 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7287 (t80) REVERT: R 156 MET cc_start: 0.7773 (mmm) cc_final: 0.7547 (mmt) REVERT: S 113 GLN cc_start: 0.6693 (mm-40) cc_final: 0.6305 (mm-40) outliers start: 31 outliers final: 24 residues processed: 167 average time/residue: 0.2062 time to fit residues: 47.2442 Evaluate side-chains 168 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8676 Z= 0.168 Angle : 0.494 7.061 11756 Z= 0.261 Chirality : 0.039 0.148 1357 Planarity : 0.003 0.032 1468 Dihedral : 5.214 53.721 1239 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.60 % Allowed : 21.46 % Favored : 74.94 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.89 (0.26), residues: 1093 helix: 2.25 (0.28), residues: 367 sheet: -0.06 (0.32), residues: 268 loop : -0.31 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE R 75 TYR 0.012 0.001 TYR B 105 ARG 0.004 0.000 ARG S 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 0.858 Fit side-chains REVERT: A 5 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7371 (mp) REVERT: A 52 GLN cc_start: 0.5831 (OUTLIER) cc_final: 0.5211 (pp30) REVERT: B 105 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7308 (t80) REVERT: R 51 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6570 (mp) REVERT: R 156 MET cc_start: 0.7761 (mmm) cc_final: 0.7530 (mmt) REVERT: S 113 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6303 (mm-40) outliers start: 32 outliers final: 26 residues processed: 163 average time/residue: 0.2123 time to fit residues: 47.4136 Evaluate side-chains 171 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.171763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137927 restraints weight = 10338.930| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.04 r_work: 0.3436 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.171 Angle : 0.495 7.035 11756 Z= 0.261 Chirality : 0.040 0.150 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.203 53.179 1239 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.60 % Allowed : 21.57 % Favored : 74.83 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.90 (0.26), residues: 1093 helix: 2.26 (0.28), residues: 367 sheet: -0.03 (0.32), residues: 268 loop : -0.31 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.023 0.001 PHE A 334 TYR 0.013 0.001 TYR B 105 ARG 0.004 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2133.52 seconds wall clock time: 39 minutes 33.18 seconds (2373.18 seconds total)