Starting phenix.real_space_refine on Tue Mar 19 03:11:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/03_2024/8adi_15363_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/03_2024/8adi_15363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/03_2024/8adi_15363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/03_2024/8adi_15363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/03_2024/8adi_15363_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/03_2024/8adi_15363_trim_updated.pdb" } resolution = 3.4 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= 0.006 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7425 2.51 5 N 2014 2.21 5 O 2317 1.98 5 H 11353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 727": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 23141 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 12144 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 29, 'TRANS': 756} Chain: "B" Number of atoms: 5393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5393 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 11, 'TRANS': 349} Chain breaks: 1 Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 845 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3348 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1292 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "F" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 119 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0AF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.93, per 1000 atoms: 0.43 Number of scatterers: 23141 At special positions: 0 Unit cell: (100.3, 133.45, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2317 8.00 N 2014 7.00 C 7425 6.00 H 11353 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.59 Conformation dependent library (CDL) restraints added in 2.5 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 17 sheets defined 19.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 56 through 68 Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 130 through 144 Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.118A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.817A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.412A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'C' and resid 33 through 36 No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 49 through 61 removed outlier: 3.650A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 160 through 188 removed outlier: 3.636A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 209 through 224 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 228 through 239 Processing helix chain 'E' and resid 52 through 58 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 100 removed outlier: 8.936A pdb=" N THR A 98 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU A 165 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER A 100 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 167 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.336A pdb=" N VAL A 339 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ASN A 276 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 341 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= D, first strand: chain 'A' and resid 425 through 431 removed outlier: 3.545A pdb=" N THR A 474 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 466 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 516 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 531 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 526 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 599 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 490 through 495 Processing sheet with id= F, first strand: chain 'A' and resid 72 through 79 removed outlier: 6.856A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.363A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.338A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.041A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.890A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.583A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.689A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.676A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.697A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 290 through 292 removed outlier: 4.011A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 331 through 333 Processing sheet with id= Q, first strand: chain 'E' and resid 32 through 34 451 hydrogen bonds defined for protein. 1257 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: 8.49 Time building geometry restraints manager: 18.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11328 1.03 - 1.22: 26 1.22 - 1.42: 5211 1.42 - 1.61: 6772 1.61 - 1.81: 62 Bond restraints: 23399 Sorted by residual: bond pdb=" C TRP F 3 " pdb=" O TRP F 3 " ideal model delta sigma weight residual 1.234 1.396 -0.162 1.23e-02 6.61e+03 1.74e+02 bond pdb=" CZ3 TRP F 3 " pdb=" HZ3 TRP F 3 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CD1 TRP F 7 " pdb=" HD1 TRP F 7 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CE3 TRP F 3 " pdb=" HE3 TRP F 3 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CZ2 TRP F 3 " pdb=" HZ2 TRP F 3 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 23394 not shown) Histogram of bond angle deviations from ideal: 91.56 - 100.07: 5 100.07 - 108.57: 7168 108.57 - 117.07: 22945 117.07 - 125.58: 11660 125.58 - 134.08: 296 Bond angle restraints: 42074 Sorted by residual: angle pdb=" CE2 0AF F 1 " pdb=" CZ2 0AF F 1 " pdb=" O1 0AF F 1 " ideal model delta sigma weight residual 123.82 105.58 18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" CH2 0AF F 1 " pdb=" CZ2 0AF F 1 " pdb=" O1 0AF F 1 " ideal model delta sigma weight residual 118.70 100.51 18.19 3.00e+00 1.11e-01 3.68e+01 angle pdb=" CA LYS F 5 " pdb=" CB LYS F 5 " pdb=" HB3 LYS F 5 " ideal model delta sigma weight residual 109.00 91.58 17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" CA TRP F 3 " pdb=" C TRP F 3 " pdb=" O TRP F 3 " ideal model delta sigma weight residual 121.36 114.66 6.70 1.20e+00 6.94e-01 3.12e+01 angle pdb=" CG LYS F 5 " pdb=" CB LYS F 5 " pdb=" HB3 LYS F 5 " ideal model delta sigma weight residual 108.00 91.56 16.44 3.00e+00 1.11e-01 3.00e+01 ... (remaining 42069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10044 17.86 - 35.73: 760 35.73 - 53.59: 233 53.59 - 71.46: 47 71.46 - 89.32: 12 Dihedral angle restraints: 11096 sinusoidal: 5978 harmonic: 5118 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -130.57 44.57 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CA TRP A 546 " pdb=" C TRP A 546 " pdb=" N ARG A 547 " pdb=" CA ARG A 547 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA SER A 425 " pdb=" C SER A 425 " pdb=" N PHE A 426 " pdb=" CA PHE A 426 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1094 0.030 - 0.061: 471 0.061 - 0.091: 92 0.091 - 0.121: 103 0.121 - 0.151: 20 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA VAL B 247 " pdb=" N VAL B 247 " pdb=" C VAL B 247 " pdb=" CB VAL B 247 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE B 164 " pdb=" N ILE B 164 " pdb=" C ILE B 164 " pdb=" CB ILE B 164 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE B 296 " pdb=" N ILE B 296 " pdb=" C ILE B 296 " pdb=" CB ILE B 296 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1777 not shown) Planarity restraints: 3589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB 0AF F 1 " 0.257 2.00e-02 2.50e+03 3.06e-01 2.57e+03 pdb=" CG 0AF F 1 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 0AF F 1 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 0AF F 1 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 0AF F 1 " -0.252 2.00e-02 2.50e+03 pdb=" CE2 0AF F 1 " -0.209 2.00e-02 2.50e+03 pdb=" CE3 0AF F 1 " 0.059 2.00e-02 2.50e+03 pdb=" CZ2 0AF F 1 " -0.321 2.00e-02 2.50e+03 pdb=" CZ3 0AF F 1 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 0AF F 1 " -0.242 2.00e-02 2.50e+03 pdb=" O1 0AF F 1 " 0.823 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 546 " -0.025 2.00e-02 2.50e+03 1.64e-02 1.07e+01 pdb=" CG TRP A 546 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 546 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 546 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 546 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 546 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 546 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 546 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 546 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 546 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 546 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP A 546 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 546 " 0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 546 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 546 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A 546 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 154 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO B 155 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.024 5.00e-02 4.00e+02 ... (remaining 3586 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.93: 82 1.93 - 2.60: 25723 2.60 - 3.27: 66718 3.27 - 3.93: 85387 3.93 - 4.60: 134760 Nonbonded interactions: 312670 Sorted by model distance: nonbonded pdb=" O ASN A 520 " pdb="HD21 ASN A 520 " model vdw 1.267 1.850 nonbonded pdb=" CH2 TRP F 3 " pdb=" CB LYS F 5 " model vdw 1.491 3.450 nonbonded pdb=" O MET A 545 " pdb=" H TYR A 548 " model vdw 1.547 1.850 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.606 1.850 nonbonded pdb=" HG SER A 502 " pdb=" OE1 GLN A 542 " model vdw 1.615 1.850 ... (remaining 312665 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=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: 2.990 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: 0.280 Extract box with map and model: 10.990 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 73.200 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 0.162 12046 Z= 0.195 Angle : 0.519 18.244 16372 Z= 0.274 Chirality : 0.042 0.151 1780 Planarity : 0.007 0.306 2155 Dihedral : 14.250 89.324 4360 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.08 % Allowed : 0.16 % Favored : 99.76 % 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: -0.36 (0.22), residues: 1488 helix: 2.47 (0.30), residues: 307 sheet: -0.75 (0.23), residues: 468 loop : -1.07 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 546 HIS 0.005 0.001 HIS D 102 PHE 0.008 0.001 PHE A 791 TYR 0.013 0.001 TYR D 184 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 731 ASN cc_start: 0.8414 (p0) cc_final: 0.8208 (p0) REVERT: B 321 ASP cc_start: 0.7425 (t0) cc_final: 0.7074 (t0) REVERT: D 146 ASP cc_start: 0.6523 (t0) cc_final: 0.6301 (t0) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.4782 time to fit residues: 82.6565 Evaluate side-chains 100 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12046 Z= 0.177 Angle : 0.438 4.830 16372 Z= 0.232 Chirality : 0.042 0.150 1780 Planarity : 0.003 0.043 2155 Dihedral : 4.016 20.814 1650 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.79 % Allowed : 3.25 % Favored : 95.96 % 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: -0.30 (0.22), residues: 1488 helix: 2.46 (0.30), residues: 310 sheet: -0.71 (0.23), residues: 469 loop : -1.02 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 546 HIS 0.010 0.001 HIS D 102 PHE 0.008 0.001 PHE A 517 TYR 0.014 0.001 TYR D 184 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 283 LEU cc_start: 0.7864 (pp) cc_final: 0.7587 (pt) REVERT: B 321 ASP cc_start: 0.7387 (t0) cc_final: 0.7007 (t0) REVERT: D 146 ASP cc_start: 0.6551 (t0) cc_final: 0.6318 (t0) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.4950 time to fit residues: 71.7848 Evaluate side-chains 101 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 375 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 45 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.0448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12046 Z= 0.154 Angle : 0.423 4.722 16372 Z= 0.224 Chirality : 0.042 0.148 1780 Planarity : 0.003 0.045 2155 Dihedral : 3.886 19.976 1650 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.87 % Allowed : 4.68 % Favored : 94.45 % 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 (0.22), residues: 1488 helix: 2.58 (0.30), residues: 309 sheet: -0.66 (0.23), residues: 475 loop : -0.93 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.006 0.001 HIS D 102 PHE 0.007 0.001 PHE A 791 TYR 0.013 0.001 TYR D 184 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 520 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8134 (t0) REVERT: A 645 GLU cc_start: 0.6203 (mp0) cc_final: 0.5915 (mp0) REVERT: B 321 ASP cc_start: 0.7434 (t0) cc_final: 0.7050 (t0) REVERT: D 62 TYR cc_start: 0.8528 (m-80) cc_final: 0.8324 (m-80) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.4981 time to fit residues: 76.1291 Evaluate side-chains 105 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 375 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12046 Z= 0.233 Angle : 0.447 4.981 16372 Z= 0.238 Chirality : 0.042 0.156 1780 Planarity : 0.003 0.046 2155 Dihedral : 3.993 20.591 1650 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.03 % Allowed : 5.47 % Favored : 93.50 % 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: -0.28 (0.22), residues: 1488 helix: 2.48 (0.30), residues: 310 sheet: -0.74 (0.23), residues: 476 loop : -0.97 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.012 0.001 PHE A 517 TYR 0.013 0.001 TYR D 184 ARG 0.003 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8104 (tm-30) REVERT: A 520 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7910 (t0) REVERT: A 538 ASN cc_start: 0.7937 (t0) cc_final: 0.7602 (t0) REVERT: A 645 GLU cc_start: 0.6249 (mp0) cc_final: 0.5948 (mp0) REVERT: B 321 ASP cc_start: 0.7491 (t0) cc_final: 0.7024 (t0) outliers start: 13 outliers final: 12 residues processed: 103 average time/residue: 0.5184 time to fit residues: 77.3581 Evaluate side-chains 107 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain E residue 28 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12046 Z= 0.338 Angle : 0.491 5.419 16372 Z= 0.264 Chirality : 0.044 0.168 1780 Planarity : 0.004 0.051 2155 Dihedral : 4.190 21.052 1650 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.11 % Allowed : 6.97 % Favored : 91.92 % 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: -0.50 (0.22), residues: 1488 helix: 2.24 (0.30), residues: 311 sheet: -0.88 (0.23), residues: 474 loop : -1.08 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 776 HIS 0.005 0.001 HIS D 102 PHE 0.014 0.001 PHE A 791 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 520 ASN cc_start: 0.8370 (t0) cc_final: 0.8132 (t0) REVERT: A 538 ASN cc_start: 0.8078 (t0) cc_final: 0.7633 (t0) REVERT: B 321 ASP cc_start: 0.7556 (t0) cc_final: 0.7107 (t0) outliers start: 14 outliers final: 14 residues processed: 101 average time/residue: 0.5064 time to fit residues: 75.2424 Evaluate side-chains 108 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain E residue 28 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12046 Z= 0.209 Angle : 0.448 5.141 16372 Z= 0.239 Chirality : 0.042 0.158 1780 Planarity : 0.003 0.051 2155 Dihedral : 4.070 21.367 1650 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.19 % Allowed : 7.77 % Favored : 91.05 % 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: -0.37 (0.22), residues: 1488 helix: 2.33 (0.30), residues: 311 sheet: -0.79 (0.23), residues: 467 loop : -1.00 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.005 0.001 HIS D 102 PHE 0.010 0.001 PHE A 517 TYR 0.012 0.001 TYR D 184 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 520 ASN cc_start: 0.8423 (t0) cc_final: 0.8185 (t0) REVERT: A 538 ASN cc_start: 0.8046 (t0) cc_final: 0.7630 (t0) REVERT: A 645 GLU cc_start: 0.6418 (mp0) cc_final: 0.6097 (mp0) outliers start: 15 outliers final: 15 residues processed: 107 average time/residue: 0.5109 time to fit residues: 79.4021 Evaluate side-chains 108 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 28 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 87 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: 0.8098 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12046 Z= 0.174 Angle : 0.437 5.023 16372 Z= 0.231 Chirality : 0.042 0.151 1780 Planarity : 0.003 0.049 2155 Dihedral : 3.973 20.846 1650 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.35 % Allowed : 8.48 % Favored : 90.17 % 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: -0.30 (0.22), residues: 1488 helix: 2.42 (0.30), residues: 311 sheet: -0.76 (0.23), residues: 468 loop : -0.96 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.010 0.001 PHE A 517 TYR 0.013 0.001 TYR D 184 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 538 ASN cc_start: 0.8001 (t0) cc_final: 0.7665 (t0) REVERT: A 645 GLU cc_start: 0.6331 (mp0) cc_final: 0.6012 (mp0) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.5121 time to fit residues: 77.1471 Evaluate side-chains 109 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 28 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12046 Z= 0.349 Angle : 0.502 5.453 16372 Z= 0.269 Chirality : 0.043 0.171 1780 Planarity : 0.004 0.051 2155 Dihedral : 4.252 21.434 1650 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.27 % Allowed : 8.80 % Favored : 89.94 % 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: -0.55 (0.21), residues: 1488 helix: 2.13 (0.30), residues: 311 sheet: -0.90 (0.23), residues: 459 loop : -1.10 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 776 HIS 0.004 0.001 HIS D 102 PHE 0.014 0.001 PHE A 791 TYR 0.014 0.001 TYR D 184 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 538 ASN cc_start: 0.8150 (t0) cc_final: 0.7689 (t0) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.5257 time to fit residues: 79.1934 Evaluate side-chains 108 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 28 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.0050 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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: 0.8107 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12046 Z= 0.172 Angle : 0.442 5.017 16372 Z= 0.234 Chirality : 0.042 0.153 1780 Planarity : 0.003 0.052 2155 Dihedral : 4.044 21.581 1650 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.19 % Allowed : 9.11 % Favored : 89.70 % 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: -0.36 (0.22), residues: 1488 helix: 2.34 (0.30), residues: 311 sheet: -0.79 (0.23), residues: 468 loop : -0.98 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.010 0.001 PHE A 517 TYR 0.013 0.001 TYR D 184 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 538 ASN cc_start: 0.8049 (t0) cc_final: 0.7726 (t0) REVERT: A 645 GLU cc_start: 0.6370 (mp0) cc_final: 0.6047 (mp0) outliers start: 15 outliers final: 15 residues processed: 103 average time/residue: 0.5862 time to fit residues: 88.4096 Evaluate side-chains 109 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 28 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 116 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12046 Z= 0.164 Angle : 0.433 4.750 16372 Z= 0.229 Chirality : 0.042 0.150 1780 Planarity : 0.003 0.047 2155 Dihedral : 3.934 20.902 1650 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.03 % Allowed : 9.51 % Favored : 89.46 % 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: -0.23 (0.22), residues: 1488 helix: 2.47 (0.30), residues: 310 sheet: -0.70 (0.23), residues: 467 loop : -0.92 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.005 0.001 HIS D 102 PHE 0.009 0.001 PHE A 517 TYR 0.013 0.001 TYR D 184 ARG 0.008 0.000 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 538 ASN cc_start: 0.8033 (t0) cc_final: 0.7708 (t0) REVERT: A 645 GLU cc_start: 0.6307 (mp0) cc_final: 0.5958 (mp0) outliers start: 13 outliers final: 13 residues processed: 105 average time/residue: 0.5423 time to fit residues: 82.9247 Evaluate side-chains 109 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 28 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.146185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111020 restraints weight = 36097.024| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.68 r_work: 0.3002 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12046 Z= 0.251 Angle : 0.458 4.967 16372 Z= 0.243 Chirality : 0.042 0.158 1780 Planarity : 0.003 0.051 2155 Dihedral : 4.031 20.951 1650 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.19 % Allowed : 9.59 % Favored : 89.22 % 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: -0.35 (0.22), residues: 1488 helix: 2.35 (0.30), residues: 311 sheet: -0.80 (0.23), residues: 469 loop : -0.97 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 776 HIS 0.004 0.001 HIS D 102 PHE 0.010 0.001 PHE A 791 TYR 0.013 0.001 TYR D 184 ARG 0.008 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4714.85 seconds wall clock time: 83 minutes 44.13 seconds (5024.13 seconds total)