Starting phenix.real_space_refine on Tue Feb 13 20:09:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/02_2024/7tof_26031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/02_2024/7tof_26031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/02_2024/7tof_26031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/02_2024/7tof_26031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/02_2024/7tof_26031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tof_26031/02_2024/7tof_26031.pdb" } resolution = 3.7 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= 0.104 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 40 5.16 5 C 4838 2.51 5 N 1318 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B TYR 437": "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: 7588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 Time building chain proxies: 4.26, per 1000 atoms: 0.56 Number of scatterers: 7588 At special positions: 0 Unit cell: (73.04, 80.51, 135.29, 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 40 16.00 O 1392 8.00 N 1318 7.00 C 4838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.3 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 42.3% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.822A pdb=" N ASP A 58 " --> pdb=" O TRP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 Proline residue: A 86 - end of helix removed outlier: 3.856A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.768A pdb=" N TYR A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.996A pdb=" N LYS A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 206 through 217 removed outlier: 3.745A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.168A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 251' Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.378A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.621A pdb=" N THR A 319 " --> pdb=" O GLY A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.557A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.037A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 47 through 58 removed outlier: 3.605A pdb=" N THR B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 58 " --> pdb=" O TRP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.554A pdb=" N LEU B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.591A pdb=" N TYR B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.895A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 206 through 217 removed outlier: 4.019A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.571A pdb=" N ARG B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.054A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 8.558A pdb=" N SER A 106 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 67 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL A 108 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY A 69 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 33 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 421 removed outlier: 8.494A pdb=" N ILE A 355 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 233 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG A 357 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A 235 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLY A 359 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE A 237 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A 358 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.221A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 166 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 168 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 421 removed outlier: 3.534A pdb=" N LEU B 420 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ILE B 480 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 405 through 407 295 hydrogen bonds defined for protein. 846 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: 2.19 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2518 1.34 - 1.46: 1498 1.46 - 1.58: 3684 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 7766 Sorted by residual: bond pdb=" CB TRP B 225 " pdb=" CG TRP B 225 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.44e+00 bond pdb=" CB GLU B 156 " pdb=" CG GLU B 156 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.56e-01 bond pdb=" CA LYS B 403 " pdb=" C LYS B 403 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.10e-02 8.26e+03 8.06e-01 bond pdb=" CG LEU A 235 " pdb=" CD1 LEU A 235 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.01e-01 bond pdb=" CA ILE B 36 " pdb=" CB ILE B 36 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.11e-02 8.12e+03 6.37e-01 ... (remaining 7761 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 229 106.51 - 113.39: 4081 113.39 - 120.28: 2875 120.28 - 127.16: 3235 127.16 - 134.04: 82 Bond angle restraints: 10502 Sorted by residual: angle pdb=" C TRP A 462 " pdb=" N ARG A 463 " pdb=" CA ARG A 463 " ideal model delta sigma weight residual 121.14 116.26 4.88 1.75e+00 3.27e-01 7.78e+00 angle pdb=" N SER A 29 " pdb=" CA SER A 29 " pdb=" C SER A 29 " ideal model delta sigma weight residual 113.43 110.35 3.08 1.26e+00 6.30e-01 5.96e+00 angle pdb=" C LEU B 214 " pdb=" N ARG B 215 " pdb=" CA ARG B 215 " ideal model delta sigma weight residual 120.68 124.78 -4.10 1.70e+00 3.46e-01 5.81e+00 angle pdb=" N LYS B 205 " pdb=" CA LYS B 205 " pdb=" CB LYS B 205 " ideal model delta sigma weight residual 113.65 110.11 3.54 1.47e+00 4.63e-01 5.81e+00 angle pdb=" N SER B 29 " pdb=" CA SER B 29 " pdb=" C SER B 29 " ideal model delta sigma weight residual 113.43 110.51 2.92 1.26e+00 6.30e-01 5.35e+00 ... (remaining 10497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 4125 16.83 - 33.66: 421 33.66 - 50.50: 86 50.50 - 67.33: 25 67.33 - 84.16: 17 Dihedral angle restraints: 4674 sinusoidal: 1944 harmonic: 2730 Sorted by residual: dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N ARG A 219 " pdb=" CA ARG A 219 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ARG B 227 " pdb=" C ARG B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL A 259 " pdb=" C VAL A 259 " pdb=" N MET A 260 " pdb=" CA MET A 260 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 617 0.028 - 0.056: 300 0.056 - 0.084: 117 0.084 - 0.112: 70 0.112 - 0.140: 20 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA VAL B 369 " pdb=" N VAL B 369 " pdb=" C VAL B 369 " pdb=" CB VAL B 369 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL B 400 " pdb=" N VAL B 400 " pdb=" C VAL B 400 " pdb=" CB VAL B 400 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL A 369 " pdb=" N VAL A 369 " pdb=" C VAL A 369 " pdb=" CB VAL A 369 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1121 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 480 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO A 481 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 222 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.61e+00 pdb=" N PRO A 223 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 352 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 353 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.027 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 229 2.71 - 3.26: 7699 3.26 - 3.81: 12707 3.81 - 4.35: 15586 4.35 - 4.90: 26279 Nonbonded interactions: 62500 Sorted by model distance: nonbonded pdb=" O TRP B 462 " pdb=" OG1 THR B 466 " model vdw 2.163 2.440 nonbonded pdb=" O ALA A 115 " pdb=" NE2 GLN A 119 " model vdw 2.197 2.520 nonbonded pdb=" OE1 GLU A 460 " pdb=" NH1 ARG A 463 " model vdw 2.234 2.520 nonbonded pdb=" NH1 ARG B 175 " pdb=" O GLU B 252 " model vdw 2.240 2.520 nonbonded pdb=" OG SER A 296 " pdb=" OE2 GLU A 345 " model vdw 2.245 2.440 ... (remaining 62495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.740 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.580 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.150 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 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 0.037 7766 Z= 0.215 Angle : 0.602 6.301 10502 Z= 0.326 Chirality : 0.044 0.140 1124 Planarity : 0.005 0.085 1374 Dihedral : 15.200 84.160 2914 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.28), residues: 930 helix: 0.31 (0.30), residues: 344 sheet: -1.18 (0.39), residues: 162 loop : -0.52 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 164 HIS 0.004 0.001 HIS B 155 PHE 0.024 0.002 PHE A 102 TYR 0.014 0.002 TYR B 484 ARG 0.006 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7477 (ptpp) cc_final: 0.7265 (ptpp) REVERT: B 87 PHE cc_start: 0.7357 (m-10) cc_final: 0.6997 (m-80) REVERT: B 137 LEU cc_start: 0.7398 (tt) cc_final: 0.7152 (tt) REVERT: B 345 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6197 (mm-30) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1909 time to fit residues: 40.1796 Evaluate side-chains 114 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 153 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7766 Z= 0.339 Angle : 0.680 8.837 10502 Z= 0.346 Chirality : 0.047 0.160 1124 Planarity : 0.005 0.060 1374 Dihedral : 4.926 21.710 1032 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.46 % Allowed : 10.49 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.74 (0.28), residues: 930 helix: 0.22 (0.29), residues: 342 sheet: -1.20 (0.37), residues: 156 loop : -0.66 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 349 HIS 0.005 0.001 HIS B 124 PHE 0.029 0.002 PHE A 102 TYR 0.019 0.003 TYR A 484 ARG 0.007 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 PHE cc_start: 0.7377 (m-10) cc_final: 0.6970 (m-80) outliers start: 12 outliers final: 7 residues processed: 146 average time/residue: 0.1805 time to fit residues: 36.7612 Evaluate side-chains 124 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7766 Z= 0.219 Angle : 0.590 7.117 10502 Z= 0.302 Chirality : 0.044 0.186 1124 Planarity : 0.005 0.051 1374 Dihedral : 4.654 20.029 1032 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.71 % Allowed : 14.15 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.28), residues: 930 helix: 0.40 (0.29), residues: 340 sheet: -1.00 (0.37), residues: 172 loop : -0.59 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 164 HIS 0.009 0.001 HIS A 451 PHE 0.020 0.002 PHE A 102 TYR 0.012 0.002 TYR A 249 ARG 0.006 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.7914 (mp0) cc_final: 0.6902 (tt0) REVERT: B 104 ARG cc_start: 0.6378 (mtp180) cc_final: 0.6161 (mtp180) REVERT: B 137 LEU cc_start: 0.7430 (tt) cc_final: 0.7229 (tt) outliers start: 14 outliers final: 9 residues processed: 141 average time/residue: 0.1648 time to fit residues: 33.0418 Evaluate side-chains 132 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7766 Z= 0.243 Angle : 0.594 7.275 10502 Z= 0.302 Chirality : 0.044 0.146 1124 Planarity : 0.005 0.053 1374 Dihedral : 4.622 20.235 1032 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.80 % Allowed : 16.22 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.57 (0.28), residues: 930 helix: 0.44 (0.29), residues: 342 sheet: -1.09 (0.38), residues: 174 loop : -0.61 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 349 HIS 0.006 0.001 HIS A 451 PHE 0.021 0.002 PHE A 102 TYR 0.014 0.002 TYR B 118 ARG 0.006 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 287 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6888 (mm-30) REVERT: A 313 ASP cc_start: 0.7551 (m-30) cc_final: 0.7192 (m-30) REVERT: A 315 GLU cc_start: 0.7949 (mp0) cc_final: 0.7034 (tt0) REVERT: B 99 GLU cc_start: 0.7386 (mp0) cc_final: 0.7185 (mp0) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 0.1613 time to fit residues: 33.0824 Evaluate side-chains 132 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 441 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 64 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 7766 Z= 0.472 Angle : 0.762 8.931 10502 Z= 0.388 Chirality : 0.049 0.162 1124 Planarity : 0.006 0.059 1374 Dihedral : 5.375 26.367 1032 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.66 % Allowed : 18.54 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.26 (0.28), residues: 930 helix: -0.18 (0.28), residues: 344 sheet: -1.74 (0.35), residues: 182 loop : -0.79 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 349 HIS 0.007 0.002 HIS B 155 PHE 0.032 0.003 PHE A 253 TYR 0.023 0.003 TYR B 107 ARG 0.006 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7864 (pttm) cc_final: 0.7507 (ptpp) REVERT: A 258 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.5043 (t0) REVERT: A 287 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 313 ASP cc_start: 0.7895 (m-30) cc_final: 0.7464 (m-30) REVERT: A 315 GLU cc_start: 0.8035 (mp0) cc_final: 0.7117 (tt0) REVERT: B 104 ARG cc_start: 0.6465 (mtp180) cc_final: 0.6121 (mtp180) REVERT: B 218 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8101 (m-40) outliers start: 30 outliers final: 19 residues processed: 149 average time/residue: 0.1721 time to fit residues: 36.0107 Evaluate side-chains 145 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7766 Z= 0.184 Angle : 0.606 10.182 10502 Z= 0.308 Chirality : 0.045 0.146 1124 Planarity : 0.004 0.060 1374 Dihedral : 4.689 20.900 1032 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.80 % Allowed : 19.76 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.80 (0.28), residues: 930 helix: 0.21 (0.29), residues: 348 sheet: -1.19 (0.38), residues: 174 loop : -0.73 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 53 HIS 0.005 0.001 HIS A 451 PHE 0.022 0.002 PHE A 102 TYR 0.011 0.001 TYR A 249 ARG 0.005 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.5664 (t70) cc_final: 0.5309 (t70) REVERT: A 313 ASP cc_start: 0.7653 (m-30) cc_final: 0.7272 (m-30) REVERT: A 315 GLU cc_start: 0.8003 (mp0) cc_final: 0.7176 (tt0) REVERT: A 404 MET cc_start: 0.6546 (ppp) cc_final: 0.6142 (ppp) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 0.1539 time to fit residues: 34.4929 Evaluate side-chains 139 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 441 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7766 Z= 0.204 Angle : 0.616 10.509 10502 Z= 0.308 Chirality : 0.045 0.203 1124 Planarity : 0.004 0.059 1374 Dihedral : 4.650 20.164 1032 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.44 % Allowed : 21.71 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.75 (0.28), residues: 930 helix: 0.33 (0.30), residues: 344 sheet: -1.14 (0.38), residues: 174 loop : -0.79 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 349 HIS 0.006 0.001 HIS A 451 PHE 0.022 0.002 PHE A 102 TYR 0.011 0.002 TYR A 118 ARG 0.005 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 258 ASP cc_start: 0.5745 (t70) cc_final: 0.5387 (t70) REVERT: A 313 ASP cc_start: 0.7733 (m-30) cc_final: 0.7330 (m-30) REVERT: A 315 GLU cc_start: 0.8027 (mp0) cc_final: 0.7224 (tt0) REVERT: B 57 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5936 (ptp-170) REVERT: B 87 PHE cc_start: 0.7785 (m-80) cc_final: 0.7156 (m-10) outliers start: 20 outliers final: 15 residues processed: 142 average time/residue: 0.1683 time to fit residues: 33.8123 Evaluate side-chains 140 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7766 Z= 0.364 Angle : 0.716 10.063 10502 Z= 0.358 Chirality : 0.048 0.206 1124 Planarity : 0.005 0.059 1374 Dihedral : 5.169 24.872 1032 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.05 % Allowed : 21.59 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.09 (0.28), residues: 930 helix: 0.06 (0.29), residues: 346 sheet: -1.65 (0.35), residues: 188 loop : -0.78 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 349 HIS 0.009 0.001 HIS A 451 PHE 0.023 0.002 PHE A 413 TYR 0.018 0.002 TYR A 484 ARG 0.008 0.001 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.7888 (m-30) cc_final: 0.7447 (m-30) REVERT: A 315 GLU cc_start: 0.8093 (mp0) cc_final: 0.7254 (tt0) REVERT: B 57 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.6028 (ptp-170) REVERT: B 87 PHE cc_start: 0.7837 (m-80) cc_final: 0.7327 (m-10) outliers start: 25 outliers final: 19 residues processed: 151 average time/residue: 0.1706 time to fit residues: 35.9334 Evaluate side-chains 147 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 54 TRP Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7766 Z= 0.188 Angle : 0.647 11.543 10502 Z= 0.323 Chirality : 0.046 0.238 1124 Planarity : 0.004 0.061 1374 Dihedral : 4.695 27.153 1032 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.20 % Allowed : 23.54 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.78 (0.28), residues: 930 helix: 0.32 (0.30), residues: 340 sheet: -1.13 (0.37), residues: 180 loop : -0.82 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 349 HIS 0.010 0.001 HIS B 186 PHE 0.021 0.001 PHE A 102 TYR 0.011 0.001 TYR A 118 ARG 0.007 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7619 (tptt) cc_final: 0.6743 (tptt) REVERT: A 258 ASP cc_start: 0.5584 (t70) cc_final: 0.5165 (t70) REVERT: A 313 ASP cc_start: 0.7705 (m-30) cc_final: 0.7308 (m-30) REVERT: A 315 GLU cc_start: 0.8002 (mp0) cc_final: 0.7194 (tt0) REVERT: B 57 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.5893 (ptp-170) REVERT: B 104 ARG cc_start: 0.6692 (mtp180) cc_final: 0.6166 (mtm180) REVERT: B 156 GLU cc_start: 0.7950 (pp20) cc_final: 0.7594 (pp20) outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 0.1715 time to fit residues: 36.2093 Evaluate side-chains 144 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 54 TRP Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 0.0020 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7766 Z= 0.181 Angle : 0.643 10.769 10502 Z= 0.321 Chirality : 0.045 0.151 1124 Planarity : 0.004 0.063 1374 Dihedral : 4.576 24.284 1032 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.83 % Allowed : 24.51 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.69 (0.28), residues: 930 helix: 0.39 (0.30), residues: 340 sheet: -0.93 (0.38), residues: 176 loop : -0.86 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.011 0.001 HIS B 155 PHE 0.021 0.002 PHE A 102 TYR 0.017 0.002 TYR A 401 ARG 0.006 0.000 ARG B 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7552 (tptt) cc_final: 0.6764 (tptt) REVERT: A 258 ASP cc_start: 0.5488 (t70) cc_final: 0.5070 (t70) REVERT: A 313 ASP cc_start: 0.7761 (m-30) cc_final: 0.7357 (m-30) REVERT: A 315 GLU cc_start: 0.7942 (mp0) cc_final: 0.7126 (tt0) REVERT: A 404 MET cc_start: 0.6672 (ppp) cc_final: 0.5963 (ppp) REVERT: B 104 ARG cc_start: 0.6614 (mtp180) cc_final: 0.6116 (mtm180) outliers start: 15 outliers final: 10 residues processed: 146 average time/residue: 0.1694 time to fit residues: 35.2087 Evaluate side-chains 142 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.218057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.188726 restraints weight = 10348.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.188875 restraints weight = 10550.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.191603 restraints weight = 8234.749| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4405 r_free = 0.4405 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7766 Z= 0.248 Angle : 0.672 11.378 10502 Z= 0.333 Chirality : 0.046 0.238 1124 Planarity : 0.004 0.061 1374 Dihedral : 4.719 22.210 1032 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.07 % Allowed : 24.27 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.28), residues: 930 helix: 0.40 (0.30), residues: 338 sheet: -1.10 (0.38), residues: 164 loop : -0.90 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 349 HIS 0.008 0.001 HIS A 451 PHE 0.023 0.002 PHE A 413 TYR 0.022 0.002 TYR B 107 ARG 0.006 0.001 ARG B 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.15 seconds wall clock time: 31 minutes 17.15 seconds (1877.15 seconds total)