Starting phenix.real_space_refine on Thu Mar 14 17:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/03_2024/8exq_28659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/03_2024/8exq_28659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/03_2024/8exq_28659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/03_2024/8exq_28659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/03_2024/8exq_28659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/03_2024/8exq_28659.pdb" } resolution = 4.9 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= 0.003 sd= 0.045 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 Zn 2 6.06 5 S 38 5.16 5 C 6112 2.51 5 N 1534 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9304 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.30, per 1000 atoms: 0.57 Number of scatterers: 9304 At special positions: 0 Unit cell: (73.9927, 108.282, 135.353, 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) Zn 2 29.99 S 38 16.00 O 1618 8.00 N 1534 7.00 C 6112 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: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 57.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 99 through 133 removed outlier: 3.571A pdb=" N ASP B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 229 through 251 removed outlier: 3.969A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 253 No H-bonds generated for 'chain 'B' and resid 252 through 253' Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.647A pdb=" N SER B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 402 removed outlier: 4.270A pdb=" N TYR B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'A' and resid 2 through 31 Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.563A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 99 through 132 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.659A pdb=" N ASN A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.620A pdb=" N ASN A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 5.426A pdb=" N ASN A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 272 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 402 removed outlier: 4.455A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLY A 525 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 514 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.457A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY B 525 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU B 514 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR A 92 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 529 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A 94 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 531 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 137 538 hydrogen bonds defined for protein. 1542 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: 2.90 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2085 1.32 - 1.46: 3022 1.46 - 1.59: 4346 1.59 - 1.73: 11 1.73 - 1.86: 68 Bond restraints: 9532 Sorted by residual: bond pdb=" CB HIS B 201 " pdb=" CG HIS B 201 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.14e+01 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.418 0.079 1.40e-02 5.10e+03 3.22e+01 bond pdb=" CB TYR B 552 " pdb=" CG TYR B 552 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB PHE A 90 " pdb=" CG PHE A 90 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.58e+01 bond pdb=" CG MET B 494 " pdb=" SD MET B 494 " ideal model delta sigma weight residual 1.803 1.678 0.125 2.50e-02 1.60e+03 2.52e+01 ... (remaining 9527 not shown) Histogram of bond angle deviations from ideal: 93.13 - 101.33: 10 101.33 - 109.53: 1736 109.53 - 117.73: 5347 117.73 - 125.93: 5601 125.93 - 134.13: 142 Bond angle restraints: 12836 Sorted by residual: angle pdb=" CA PHE A 313 " pdb=" CB PHE A 313 " pdb=" CG PHE A 313 " ideal model delta sigma weight residual 113.80 105.83 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" CA ASP A 550 " pdb=" CB ASP A 550 " pdb=" CG ASP A 550 " ideal model delta sigma weight residual 112.60 120.57 -7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" C SER B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.01e+00 9.80e-01 6.13e+01 angle pdb=" C TYR B 419 " pdb=" N PRO B 420 " pdb=" CA PRO B 420 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.02e+00 9.61e-01 6.11e+01 angle pdb=" C TYR A 419 " pdb=" N PRO A 420 " pdb=" CA PRO A 420 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.02e+00 9.61e-01 5.96e+01 ... (remaining 12831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5476 17.91 - 35.81: 176 35.81 - 53.72: 26 53.72 - 71.62: 9 71.62 - 89.53: 7 Dihedral angle restraints: 5694 sinusoidal: 2374 harmonic: 3320 Sorted by residual: dihedral pdb=" C ILE B 48 " pdb=" N ILE B 48 " pdb=" CA ILE B 48 " pdb=" CB ILE B 48 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C PHE B 501 " pdb=" N PHE B 501 " pdb=" CA PHE B 501 " pdb=" CB PHE B 501 " ideal model delta harmonic sigma weight residual -122.60 -113.60 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C TYR B 385 " pdb=" N TYR B 385 " pdb=" CA TYR B 385 " pdb=" CB TYR B 385 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 923 0.095 - 0.189: 364 0.189 - 0.284: 87 0.284 - 0.379: 13 0.379 - 0.473: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB ILE B 531 " pdb=" CA ILE B 531 " pdb=" CG1 ILE B 531 " pdb=" CG2 ILE B 531 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA PHE A 313 " pdb=" N PHE A 313 " pdb=" C PHE A 313 " pdb=" CB PHE A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ASN B 436 " pdb=" N ASN B 436 " pdb=" C ASN B 436 " pdb=" CB ASN B 436 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1385 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 36 " -0.077 2.00e-02 2.50e+03 4.24e-02 3.60e+01 pdb=" CG TYR A 36 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 36 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 36 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 36 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 36 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 36 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 36 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 540 " -0.075 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP A 540 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 540 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 540 " 0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 540 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 540 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 540 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 540 " -0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 540 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 540 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 373 " 0.064 2.00e-02 2.50e+03 3.95e-02 3.12e+01 pdb=" CG TYR B 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 373 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 373 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 373 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR B 373 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR B 373 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 373 " 0.068 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 67 2.58 - 3.16: 8618 3.16 - 3.74: 15153 3.74 - 4.32: 22622 4.32 - 4.90: 34188 Nonbonded interactions: 80648 Sorted by model distance: nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.002 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.033 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.044 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.061 2.230 nonbonded pdb=" CD GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.345 2.460 ... (remaining 80643 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 Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 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: 0.010 Normalize map: mean=0, sd=1: 0.070 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: 1.030 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.890 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 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 : 0.020 0.130 9532 Z= 1.264 Angle : 1.739 10.276 12836 Z= 1.191 Chirality : 0.104 0.473 1388 Planarity : 0.009 0.044 1574 Dihedral : 10.285 89.529 3554 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 0.34 (0.24), residues: 1100 helix: 0.79 (0.20), residues: 534 sheet: -0.15 (0.46), residues: 117 loop : -0.21 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.013 TRP A 540 HIS 0.009 0.002 HIS A 153 PHE 0.037 0.007 PHE A 274 TYR 0.077 0.012 TYR A 36 ARG 0.007 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8886 (t80) cc_final: 0.7920 (t80) REVERT: A 131 LEU cc_start: 0.9043 (mt) cc_final: 0.8838 (mp) REVERT: A 143 LYS cc_start: 0.8863 (tttm) cc_final: 0.8445 (tmtt) REVERT: A 147 ASP cc_start: 0.8624 (m-30) cc_final: 0.8340 (m-30) REVERT: A 149 ILE cc_start: 0.9315 (mt) cc_final: 0.8812 (mm) REVERT: A 180 ILE cc_start: 0.8271 (mt) cc_final: 0.7615 (mt) REVERT: A 181 LEU cc_start: 0.9043 (mp) cc_final: 0.8751 (mp) REVERT: A 208 ASN cc_start: 0.9097 (m-40) cc_final: 0.7563 (m110) REVERT: A 215 ILE cc_start: 0.8958 (mt) cc_final: 0.8726 (mt) REVERT: A 216 ILE cc_start: 0.9672 (mt) cc_final: 0.9248 (mt) REVERT: A 220 PHE cc_start: 0.7931 (m-10) cc_final: 0.7512 (m-80) REVERT: A 227 ASN cc_start: 0.8976 (t0) cc_final: 0.8402 (t0) REVERT: A 248 PHE cc_start: 0.6596 (m-80) cc_final: 0.6072 (m-80) REVERT: A 292 LYS cc_start: 0.8466 (tptt) cc_final: 0.7860 (tttm) REVERT: A 296 ILE cc_start: 0.9503 (mt) cc_final: 0.9228 (mm) REVERT: A 297 ASN cc_start: 0.8594 (m-40) cc_final: 0.8230 (m110) REVERT: A 311 LEU cc_start: 0.9239 (pp) cc_final: 0.8840 (mp) REVERT: A 368 MET cc_start: -0.2061 (tpt) cc_final: -0.2607 (ttm) REVERT: A 462 ASN cc_start: 0.5872 (t0) cc_final: 0.5219 (m-40) REVERT: A 553 TYR cc_start: 0.3296 (m-80) cc_final: 0.1548 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1841 time to fit residues: 43.9755 Evaluate side-chains 114 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.0050 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 0.0030 overall best weight: 0.1208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 282 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4437 moved from start: 1.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9532 Z= 0.247 Angle : 0.760 8.448 12836 Z= 0.420 Chirality : 0.047 0.155 1388 Planarity : 0.005 0.039 1574 Dihedral : 5.606 30.991 1208 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.77 % Allowed : 3.47 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1100 helix: 1.31 (0.21), residues: 566 sheet: -0.00 (0.46), residues: 122 loop : -0.76 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 414 HIS 0.009 0.002 HIS A 213 PHE 0.038 0.003 PHE A 14 TYR 0.027 0.002 TYR B 524 ARG 0.005 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8618 (pttp) cc_final: 0.7928 (pttt) REVERT: A 31 ASN cc_start: 0.8690 (m-40) cc_final: 0.8225 (p0) REVERT: A 110 TRP cc_start: 0.7438 (t60) cc_final: 0.6859 (t60) REVERT: A 126 LEU cc_start: 0.9276 (mt) cc_final: 0.8879 (mt) REVERT: A 127 TYR cc_start: 0.7695 (t80) cc_final: 0.7142 (t80) REVERT: A 130 TYR cc_start: 0.7783 (m-10) cc_final: 0.7563 (m-80) REVERT: A 208 ASN cc_start: 0.8549 (m-40) cc_final: 0.8169 (p0) REVERT: A 227 ASN cc_start: 0.8473 (t0) cc_final: 0.8168 (t0) REVERT: A 233 VAL cc_start: 0.8700 (m) cc_final: 0.8435 (m) REVERT: A 244 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7262 (mm-30) REVERT: A 295 LEU cc_start: 0.9291 (mt) cc_final: 0.8811 (mt) REVERT: A 365 MET cc_start: 0.0816 (tmm) cc_final: -0.0058 (tpp) REVERT: A 368 MET cc_start: -0.1327 (tpt) cc_final: -0.1800 (ttm) REVERT: A 462 ASN cc_start: 0.4952 (t0) cc_final: 0.4337 (m-40) outliers start: 4 outliers final: 2 residues processed: 162 average time/residue: 0.1670 time to fit residues: 34.0914 Evaluate side-chains 122 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 83 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.0000 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 0.0000 chunk 80 optimal weight: 8.9990 overall best weight: 0.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 557 HIS A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4474 moved from start: 1.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9532 Z= 0.186 Angle : 0.650 6.991 12836 Z= 0.362 Chirality : 0.043 0.216 1388 Planarity : 0.004 0.044 1574 Dihedral : 5.246 24.759 1208 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.39 % Allowed : 3.28 % Favored : 96.33 % 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: -0.01 (0.25), residues: 1100 helix: 0.66 (0.21), residues: 566 sheet: -0.01 (0.43), residues: 136 loop : -0.84 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 424 HIS 0.005 0.001 HIS B 418 PHE 0.047 0.002 PHE A 14 TYR 0.020 0.002 TYR B 524 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7501 (t60) cc_final: 0.7137 (t60) REVERT: A 121 PHE cc_start: 0.8249 (t80) cc_final: 0.7696 (t80) REVERT: A 126 LEU cc_start: 0.9238 (mt) cc_final: 0.8670 (mt) REVERT: A 127 TYR cc_start: 0.7795 (t80) cc_final: 0.6611 (t80) REVERT: A 130 TYR cc_start: 0.7591 (m-10) cc_final: 0.7369 (m-80) REVERT: A 132 LYS cc_start: 0.8433 (ptmm) cc_final: 0.8187 (ptmm) REVERT: A 198 ILE cc_start: 0.8918 (pt) cc_final: 0.8357 (pt) REVERT: A 199 ILE cc_start: 0.9468 (mm) cc_final: 0.8974 (mm) REVERT: A 208 ASN cc_start: 0.9062 (m-40) cc_final: 0.7957 (m-40) REVERT: A 212 LEU cc_start: 0.8981 (tt) cc_final: 0.7962 (tp) REVERT: A 213 HIS cc_start: 0.8347 (m90) cc_final: 0.8136 (m-70) REVERT: A 222 ILE cc_start: 0.8756 (pt) cc_final: 0.8511 (pt) REVERT: A 227 ASN cc_start: 0.8467 (t0) cc_final: 0.7932 (t0) REVERT: A 233 VAL cc_start: 0.8760 (m) cc_final: 0.8521 (m) REVERT: A 241 ASN cc_start: 0.8405 (t0) cc_final: 0.7983 (t0) REVERT: A 292 LYS cc_start: 0.8034 (tptt) cc_final: 0.6583 (tptt) REVERT: A 294 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8518 (mmm-85) REVERT: A 295 LEU cc_start: 0.9191 (mt) cc_final: 0.8703 (mt) REVERT: A 296 ILE cc_start: 0.8869 (pt) cc_final: 0.8058 (pt) REVERT: A 297 ASN cc_start: 0.8382 (m-40) cc_final: 0.8097 (m-40) REVERT: A 302 ASN cc_start: 0.8328 (t0) cc_final: 0.7883 (t0) REVERT: A 317 PHE cc_start: 0.8914 (m-80) cc_final: 0.8590 (m-80) REVERT: A 322 MET cc_start: 0.9217 (mpp) cc_final: 0.9009 (mmt) REVERT: A 368 MET cc_start: -0.2209 (tpt) cc_final: -0.3037 (ttp) outliers start: 2 outliers final: 2 residues processed: 140 average time/residue: 0.1504 time to fit residues: 26.7743 Evaluate side-chains 119 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 487 GLN A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4543 moved from start: 1.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9532 Z= 0.173 Angle : 0.639 6.380 12836 Z= 0.357 Chirality : 0.042 0.171 1388 Planarity : 0.004 0.040 1574 Dihedral : 4.946 21.205 1208 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1100 helix: 0.23 (0.20), residues: 568 sheet: 0.13 (0.44), residues: 136 loop : -1.17 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 414 HIS 0.006 0.001 HIS A 418 PHE 0.045 0.002 PHE B 14 TYR 0.022 0.002 TYR B 544 ARG 0.002 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7956 (m-80) cc_final: 0.7609 (m-80) REVERT: A 110 TRP cc_start: 0.7734 (t60) cc_final: 0.7172 (t60) REVERT: A 122 LEU cc_start: 0.9256 (tp) cc_final: 0.8910 (tp) REVERT: A 126 LEU cc_start: 0.9096 (mt) cc_final: 0.8660 (mt) REVERT: A 127 TYR cc_start: 0.7811 (t80) cc_final: 0.7476 (t80) REVERT: A 130 TYR cc_start: 0.7698 (m-10) cc_final: 0.7355 (m-80) REVERT: A 153 HIS cc_start: 0.7466 (m90) cc_final: 0.7130 (m90) REVERT: A 172 THR cc_start: 0.8985 (m) cc_final: 0.8630 (m) REVERT: A 174 TRP cc_start: 0.7619 (t60) cc_final: 0.7369 (t60) REVERT: A 198 ILE cc_start: 0.9060 (pt) cc_final: 0.8538 (pt) REVERT: A 199 ILE cc_start: 0.9470 (mm) cc_final: 0.8996 (mm) REVERT: A 208 ASN cc_start: 0.8765 (m-40) cc_final: 0.8006 (m-40) REVERT: A 212 LEU cc_start: 0.9153 (tt) cc_final: 0.8900 (mt) REVERT: A 227 ASN cc_start: 0.8464 (t0) cc_final: 0.7867 (t0) REVERT: A 233 VAL cc_start: 0.8791 (m) cc_final: 0.8567 (m) REVERT: A 244 GLU cc_start: 0.8779 (mm-30) cc_final: 0.7352 (mm-30) REVERT: A 247 ARG cc_start: 0.8720 (ttp-170) cc_final: 0.7924 (ttp-170) REVERT: A 292 LYS cc_start: 0.8289 (tptt) cc_final: 0.7092 (tptt) REVERT: A 294 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8296 (mmm-85) REVERT: A 295 LEU cc_start: 0.9177 (mt) cc_final: 0.8721 (mt) REVERT: A 296 ILE cc_start: 0.8845 (pt) cc_final: 0.8109 (pt) REVERT: A 302 ASN cc_start: 0.8422 (t0) cc_final: 0.7926 (t0) REVERT: A 317 PHE cc_start: 0.8836 (m-80) cc_final: 0.8586 (m-80) REVERT: A 320 LEU cc_start: 0.9351 (mm) cc_final: 0.9063 (mm) REVERT: A 365 MET cc_start: 0.0662 (tmm) cc_final: 0.0233 (tpp) REVERT: A 368 MET cc_start: -0.1105 (tpt) cc_final: -0.1912 (ttm) REVERT: A 495 MET cc_start: 0.5193 (mmt) cc_final: 0.4469 (mmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1399 time to fit residues: 24.6347 Evaluate side-chains 120 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 231 HIS A 239 HIS A 285 ASN A 567 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4537 moved from start: 1.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9532 Z= 0.162 Angle : 0.613 7.288 12836 Z= 0.335 Chirality : 0.041 0.153 1388 Planarity : 0.004 0.043 1574 Dihedral : 4.753 23.262 1208 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.19 % Allowed : 2.51 % Favored : 97.30 % 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: -0.43 (0.24), residues: 1100 helix: 0.31 (0.20), residues: 570 sheet: 0.29 (0.47), residues: 124 loop : -1.22 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 414 HIS 0.005 0.001 HIS A 231 PHE 0.029 0.002 PHE B 14 TYR 0.019 0.001 TYR A 441 ARG 0.002 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7312 (t60) cc_final: 0.6779 (t60) REVERT: A 122 LEU cc_start: 0.9211 (tp) cc_final: 0.8960 (tp) REVERT: A 126 LEU cc_start: 0.9056 (mt) cc_final: 0.8542 (mt) REVERT: A 130 TYR cc_start: 0.7796 (m-10) cc_final: 0.7469 (m-80) REVERT: A 132 LYS cc_start: 0.8756 (pptt) cc_final: 0.8535 (ptmm) REVERT: A 138 LEU cc_start: 0.7325 (mt) cc_final: 0.6933 (mt) REVERT: A 141 ASN cc_start: 0.8921 (m-40) cc_final: 0.8424 (p0) REVERT: A 153 HIS cc_start: 0.7627 (m90) cc_final: 0.7336 (m90) REVERT: A 178 TYR cc_start: 0.5088 (m-80) cc_final: 0.4515 (m-80) REVERT: A 198 ILE cc_start: 0.9060 (pt) cc_final: 0.8494 (pt) REVERT: A 199 ILE cc_start: 0.9486 (mm) cc_final: 0.9013 (mm) REVERT: A 202 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 208 ASN cc_start: 0.8895 (m-40) cc_final: 0.8264 (m110) REVERT: A 227 ASN cc_start: 0.8507 (t0) cc_final: 0.7744 (t0) REVERT: A 239 HIS cc_start: 0.8321 (m90) cc_final: 0.8049 (m90) REVERT: A 244 GLU cc_start: 0.8866 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 247 ARG cc_start: 0.8674 (ttp-170) cc_final: 0.8044 (ttp-170) REVERT: A 248 PHE cc_start: 0.6239 (m-10) cc_final: 0.5731 (m-10) REVERT: A 292 LYS cc_start: 0.8491 (tptt) cc_final: 0.8133 (tptt) REVERT: A 294 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8308 (mmm-85) REVERT: A 295 LEU cc_start: 0.9177 (mt) cc_final: 0.8791 (mt) REVERT: A 302 ASN cc_start: 0.8576 (t0) cc_final: 0.8047 (t0) REVERT: A 320 LEU cc_start: 0.9304 (mm) cc_final: 0.8884 (mm) REVERT: A 365 MET cc_start: 0.0660 (tmm) cc_final: 0.0165 (tpp) REVERT: A 368 MET cc_start: -0.1132 (tpt) cc_final: -0.1649 (ttm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1433 time to fit residues: 25.9817 Evaluate side-chains 108 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 106 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 500 HIS A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4633 moved from start: 1.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9532 Z= 0.165 Angle : 0.606 6.511 12836 Z= 0.341 Chirality : 0.040 0.146 1388 Planarity : 0.004 0.040 1574 Dihedral : 4.629 19.071 1208 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -0.29 (0.24), residues: 1100 helix: 0.42 (0.20), residues: 570 sheet: 0.31 (0.45), residues: 136 loop : -1.18 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 414 HIS 0.006 0.001 HIS A 213 PHE 0.063 0.002 PHE A 14 TYR 0.019 0.002 TYR B 544 ARG 0.003 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8007 (m100) cc_final: 0.7054 (m-90) REVERT: A 110 TRP cc_start: 0.7370 (t60) cc_final: 0.6885 (t60) REVERT: A 117 LEU cc_start: 0.9100 (mt) cc_final: 0.8815 (mt) REVERT: A 122 LEU cc_start: 0.9266 (tp) cc_final: 0.9061 (tt) REVERT: A 126 LEU cc_start: 0.9021 (mt) cc_final: 0.8481 (mt) REVERT: A 130 TYR cc_start: 0.8077 (m-10) cc_final: 0.7768 (m-80) REVERT: A 132 LYS cc_start: 0.9088 (pptt) cc_final: 0.8513 (ptmm) REVERT: A 141 ASN cc_start: 0.8868 (m-40) cc_final: 0.8473 (p0) REVERT: A 153 HIS cc_start: 0.7777 (m90) cc_final: 0.7364 (m90) REVERT: A 198 ILE cc_start: 0.9108 (pt) cc_final: 0.8563 (pt) REVERT: A 199 ILE cc_start: 0.9556 (mm) cc_final: 0.9121 (mm) REVERT: A 208 ASN cc_start: 0.8807 (m-40) cc_final: 0.8125 (m110) REVERT: A 218 ASN cc_start: 0.8658 (t0) cc_final: 0.8044 (t0) REVERT: A 244 GLU cc_start: 0.8886 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 247 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.7844 (ttp-170) REVERT: A 248 PHE cc_start: 0.6321 (m-10) cc_final: 0.6032 (m-10) REVERT: A 255 LYS cc_start: 0.9385 (mtmt) cc_final: 0.8925 (mtmm) REVERT: A 269 VAL cc_start: 0.8833 (m) cc_final: 0.8462 (p) REVERT: A 275 PHE cc_start: 0.7038 (t80) cc_final: 0.6815 (t80) REVERT: A 292 LYS cc_start: 0.8315 (tptt) cc_final: 0.7856 (tptt) REVERT: A 294 ARG cc_start: 0.8725 (mtp180) cc_final: 0.8346 (mmm-85) REVERT: A 295 LEU cc_start: 0.9204 (mt) cc_final: 0.8810 (mt) REVERT: A 302 ASN cc_start: 0.8479 (t0) cc_final: 0.8063 (t0) REVERT: A 317 PHE cc_start: 0.8540 (m-10) cc_final: 0.7859 (m-80) REVERT: A 320 LEU cc_start: 0.9350 (mm) cc_final: 0.8992 (mm) REVERT: A 322 MET cc_start: 0.9467 (mpp) cc_final: 0.9160 (mpp) REVERT: A 368 MET cc_start: -0.1147 (tpt) cc_final: -0.3066 (ptp) REVERT: A 579 MET cc_start: 0.0473 (tpt) cc_final: -0.0672 (ttt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1398 time to fit residues: 24.6198 Evaluate side-chains 106 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4536 moved from start: 1.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9532 Z= 0.170 Angle : 0.651 9.244 12836 Z= 0.357 Chirality : 0.042 0.159 1388 Planarity : 0.004 0.042 1574 Dihedral : 4.611 17.360 1208 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 0.19 % Allowed : 1.35 % Favored : 98.46 % 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: -0.46 (0.24), residues: 1100 helix: 0.37 (0.20), residues: 568 sheet: 0.18 (0.47), residues: 124 loop : -1.35 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 414 HIS 0.003 0.001 HIS B 282 PHE 0.036 0.001 PHE B 14 TYR 0.016 0.001 TYR B 544 ARG 0.002 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8126 (tpt90) cc_final: 0.7830 (tpt90) REVERT: A 39 TRP cc_start: 0.7884 (m100) cc_final: 0.6924 (m-90) REVERT: A 110 TRP cc_start: 0.7361 (t60) cc_final: 0.7035 (t60) REVERT: A 117 LEU cc_start: 0.9108 (mt) cc_final: 0.8860 (mt) REVERT: A 122 LEU cc_start: 0.9256 (tp) cc_final: 0.9031 (tt) REVERT: A 126 LEU cc_start: 0.8945 (mt) cc_final: 0.8425 (mt) REVERT: A 130 TYR cc_start: 0.7590 (m-10) cc_final: 0.7354 (m-80) REVERT: A 138 LEU cc_start: 0.7107 (mt) cc_final: 0.6774 (mt) REVERT: A 141 ASN cc_start: 0.8856 (m-40) cc_final: 0.8315 (p0) REVERT: A 153 HIS cc_start: 0.7612 (m90) cc_final: 0.7231 (m90) REVERT: A 198 ILE cc_start: 0.9074 (pt) cc_final: 0.8457 (pt) REVERT: A 199 ILE cc_start: 0.9494 (mm) cc_final: 0.9045 (mm) REVERT: A 208 ASN cc_start: 0.8627 (m-40) cc_final: 0.7726 (m110) REVERT: A 213 HIS cc_start: 0.8019 (m90) cc_final: 0.7535 (m90) REVERT: A 218 ASN cc_start: 0.8685 (t0) cc_final: 0.8150 (t0) REVERT: A 244 GLU cc_start: 0.8964 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 248 PHE cc_start: 0.6282 (m-10) cc_final: 0.6012 (m-10) REVERT: A 269 VAL cc_start: 0.8774 (m) cc_final: 0.8362 (p) REVERT: A 292 LYS cc_start: 0.8170 (tptt) cc_final: 0.7667 (tptt) REVERT: A 294 ARG cc_start: 0.8680 (mtp180) cc_final: 0.8269 (mmm-85) REVERT: A 295 LEU cc_start: 0.9186 (mt) cc_final: 0.8776 (mt) REVERT: A 317 PHE cc_start: 0.8490 (m-10) cc_final: 0.7954 (m-80) REVERT: A 322 MET cc_start: 0.9365 (mpp) cc_final: 0.9156 (mpp) REVERT: A 368 MET cc_start: -0.1814 (tpt) cc_final: -0.3680 (ptp) REVERT: A 579 MET cc_start: -0.0289 (tpt) cc_final: -0.0814 (ttt) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1503 time to fit residues: 25.2411 Evaluate side-chains 114 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.0020 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 0.0070 chunk 101 optimal weight: 0.0000 chunk 92 optimal weight: 0.0020 overall best weight: 0.1418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4522 moved from start: 1.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9532 Z= 0.170 Angle : 0.634 6.833 12836 Z= 0.343 Chirality : 0.041 0.159 1388 Planarity : 0.004 0.039 1574 Dihedral : 4.477 18.922 1208 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.55 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1100 helix: 0.54 (0.20), residues: 566 sheet: 0.14 (0.47), residues: 124 loop : -1.47 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 414 HIS 0.003 0.001 HIS A 239 PHE 0.038 0.001 PHE A 14 TYR 0.017 0.001 TYR A 544 ARG 0.001 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.7819 (m100) cc_final: 0.6800 (m-90) REVERT: A 110 TRP cc_start: 0.7375 (t60) cc_final: 0.7112 (t60) REVERT: A 117 LEU cc_start: 0.9116 (mt) cc_final: 0.8878 (mt) REVERT: A 122 LEU cc_start: 0.9229 (tp) cc_final: 0.8991 (tp) REVERT: A 126 LEU cc_start: 0.8921 (mt) cc_final: 0.8466 (mt) REVERT: A 130 TYR cc_start: 0.8170 (m-10) cc_final: 0.7747 (m-80) REVERT: A 138 LEU cc_start: 0.7263 (mt) cc_final: 0.6830 (mt) REVERT: A 141 ASN cc_start: 0.8749 (m-40) cc_final: 0.8295 (p0) REVERT: A 198 ILE cc_start: 0.9102 (pt) cc_final: 0.8459 (pt) REVERT: A 199 ILE cc_start: 0.9497 (mm) cc_final: 0.9063 (mm) REVERT: A 208 ASN cc_start: 0.8710 (m-40) cc_final: 0.7822 (m110) REVERT: A 213 HIS cc_start: 0.7917 (m90) cc_final: 0.7469 (m90) REVERT: A 218 ASN cc_start: 0.8694 (t0) cc_final: 0.8150 (t0) REVERT: A 244 GLU cc_start: 0.9027 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 248 PHE cc_start: 0.6191 (m-10) cc_final: 0.5921 (m-10) REVERT: A 269 VAL cc_start: 0.8757 (m) cc_final: 0.8388 (p) REVERT: A 292 LYS cc_start: 0.7623 (tptt) cc_final: 0.6991 (tptt) REVERT: A 294 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8262 (mmm-85) REVERT: A 295 LEU cc_start: 0.9182 (mt) cc_final: 0.8772 (mt) REVERT: A 325 GLN cc_start: 0.8878 (pm20) cc_final: 0.8660 (pm20) REVERT: A 368 MET cc_start: -0.1624 (tpt) cc_final: -0.2051 (ttp) REVERT: A 579 MET cc_start: 0.0519 (tpt) cc_final: 0.0292 (ttt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1546 time to fit residues: 26.6914 Evaluate side-chains 108 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.0010 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 moved from start: 1.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9532 Z= 0.169 Angle : 0.644 9.408 12836 Z= 0.350 Chirality : 0.042 0.175 1388 Planarity : 0.004 0.037 1574 Dihedral : 4.358 19.907 1208 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.55 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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 (0.24), residues: 1100 helix: 0.63 (0.21), residues: 570 sheet: 0.25 (0.48), residues: 120 loop : -1.58 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 174 HIS 0.003 0.001 HIS B 239 PHE 0.040 0.001 PHE A 14 TYR 0.015 0.001 TYR A 544 ARG 0.001 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8266 (t80) cc_final: 0.7981 (t80) REVERT: A 39 TRP cc_start: 0.7774 (m100) cc_final: 0.7521 (m100) REVERT: A 110 TRP cc_start: 0.7408 (t60) cc_final: 0.7109 (t60) REVERT: A 117 LEU cc_start: 0.9115 (mt) cc_final: 0.8869 (mt) REVERT: A 122 LEU cc_start: 0.9179 (tp) cc_final: 0.8744 (tp) REVERT: A 126 LEU cc_start: 0.8941 (mt) cc_final: 0.8371 (mt) REVERT: A 130 TYR cc_start: 0.8355 (m-10) cc_final: 0.7829 (m-80) REVERT: A 138 LEU cc_start: 0.6623 (mt) cc_final: 0.5994 (mt) REVERT: A 141 ASN cc_start: 0.8752 (m-40) cc_final: 0.8389 (m110) REVERT: A 198 ILE cc_start: 0.9137 (pt) cc_final: 0.8462 (pt) REVERT: A 199 ILE cc_start: 0.9493 (mm) cc_final: 0.9111 (mm) REVERT: A 208 ASN cc_start: 0.8596 (m-40) cc_final: 0.8087 (m110) REVERT: A 213 HIS cc_start: 0.7584 (m90) cc_final: 0.7333 (m170) REVERT: A 218 ASN cc_start: 0.8717 (t0) cc_final: 0.8196 (t0) REVERT: A 233 VAL cc_start: 0.8709 (m) cc_final: 0.8430 (m) REVERT: A 244 GLU cc_start: 0.8910 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 248 PHE cc_start: 0.6280 (m-10) cc_final: 0.6080 (m-10) REVERT: A 269 VAL cc_start: 0.8804 (m) cc_final: 0.8461 (p) REVERT: A 291 LEU cc_start: 0.8064 (tp) cc_final: 0.7545 (tp) REVERT: A 292 LYS cc_start: 0.8006 (tptt) cc_final: 0.7540 (tptt) REVERT: A 294 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8236 (mmm-85) REVERT: A 295 LEU cc_start: 0.9178 (mt) cc_final: 0.8503 (mt) REVERT: A 317 PHE cc_start: 0.9113 (m-80) cc_final: 0.8662 (m-10) REVERT: A 330 MET cc_start: -0.3019 (ttt) cc_final: -0.3224 (ttt) REVERT: A 368 MET cc_start: -0.0459 (tpt) cc_final: -0.3256 (ptp) REVERT: A 579 MET cc_start: 0.0734 (tpt) cc_final: -0.0042 (ttt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1467 time to fit residues: 25.9528 Evaluate side-chains 112 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 0.0970 chunk 9 optimal weight: 0.0970 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 0.0070 chunk 69 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4508 moved from start: 1.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9532 Z= 0.158 Angle : 0.655 12.662 12836 Z= 0.349 Chirality : 0.042 0.175 1388 Planarity : 0.004 0.036 1574 Dihedral : 4.414 21.497 1208 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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 (0.24), residues: 1100 helix: 0.61 (0.20), residues: 570 sheet: 0.36 (0.47), residues: 124 loop : -1.61 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 174 HIS 0.004 0.001 HIS A 282 PHE 0.036 0.002 PHE B 14 TYR 0.016 0.001 TYR B 544 ARG 0.001 0.000 ARG B 411 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8101 (t80) cc_final: 0.7494 (t80) REVERT: A 39 TRP cc_start: 0.7698 (m100) cc_final: 0.7494 (m100) REVERT: A 42 THR cc_start: 0.8671 (p) cc_final: 0.8381 (p) REVERT: A 110 TRP cc_start: 0.7440 (t60) cc_final: 0.7160 (t60) REVERT: A 117 LEU cc_start: 0.9136 (mt) cc_final: 0.8889 (mt) REVERT: A 122 LEU cc_start: 0.9149 (tp) cc_final: 0.8724 (tp) REVERT: A 126 LEU cc_start: 0.8828 (mt) cc_final: 0.8309 (mt) REVERT: A 130 TYR cc_start: 0.8328 (m-10) cc_final: 0.7819 (m-80) REVERT: A 138 LEU cc_start: 0.6791 (mt) cc_final: 0.6102 (mt) REVERT: A 141 ASN cc_start: 0.8643 (m-40) cc_final: 0.8262 (m110) REVERT: A 178 TYR cc_start: 0.5499 (m-10) cc_final: 0.5167 (m-80) REVERT: A 188 LYS cc_start: 0.9269 (mmtm) cc_final: 0.8929 (tppt) REVERT: A 198 ILE cc_start: 0.9144 (pt) cc_final: 0.8455 (pt) REVERT: A 199 ILE cc_start: 0.9558 (mm) cc_final: 0.9093 (mm) REVERT: A 208 ASN cc_start: 0.8519 (m-40) cc_final: 0.7896 (m110) REVERT: A 213 HIS cc_start: 0.7530 (m90) cc_final: 0.7087 (m-70) REVERT: A 217 PHE cc_start: 0.8570 (m-80) cc_final: 0.8014 (m-80) REVERT: A 218 ASN cc_start: 0.8759 (t0) cc_final: 0.8184 (t0) REVERT: A 233 VAL cc_start: 0.8653 (m) cc_final: 0.8427 (m) REVERT: A 244 GLU cc_start: 0.8902 (mm-30) cc_final: 0.7083 (mm-30) REVERT: A 247 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.7982 (tmm160) REVERT: A 248 PHE cc_start: 0.6209 (m-10) cc_final: 0.5828 (m-10) REVERT: A 269 VAL cc_start: 0.8830 (m) cc_final: 0.8452 (p) REVERT: A 291 LEU cc_start: 0.8097 (tp) cc_final: 0.7589 (tp) REVERT: A 292 LYS cc_start: 0.7504 (tptt) cc_final: 0.6934 (tptt) REVERT: A 294 ARG cc_start: 0.8651 (mtp180) cc_final: 0.8210 (mmm-85) REVERT: A 295 LEU cc_start: 0.9131 (mt) cc_final: 0.8475 (mt) REVERT: A 368 MET cc_start: -0.0486 (tpt) cc_final: -0.3198 (ptp) REVERT: A 579 MET cc_start: 0.0946 (tpt) cc_final: -0.0090 (ttt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1467 time to fit residues: 25.0792 Evaluate side-chains 108 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 0.0870 chunk 24 optimal weight: 0.1980 chunk 87 optimal weight: 0.0030 chunk 36 optimal weight: 0.4980 chunk 89 optimal weight: 0.0060 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.0030 chunk 63 optimal weight: 0.8980 overall best weight: 0.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.189423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.146611 restraints weight = 13698.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.151084 restraints weight = 9216.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.154179 restraints weight = 6696.854| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 1.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9532 Z= 0.160 Angle : 0.665 10.527 12836 Z= 0.356 Chirality : 0.043 0.163 1388 Planarity : 0.004 0.036 1574 Dihedral : 4.379 21.900 1208 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.55 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.38 (0.24), residues: 1100 helix: 0.63 (0.21), residues: 572 sheet: 0.39 (0.48), residues: 124 loop : -1.74 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 414 HIS 0.003 0.001 HIS B 282 PHE 0.040 0.002 PHE B 14 TYR 0.015 0.001 TYR B 544 ARG 0.001 0.000 ARG A 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.58 seconds wall clock time: 32 minutes 8.08 seconds (1928.08 seconds total)