Starting phenix.real_space_refine on Wed Feb 14 07:07:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/02_2024/8ext_28662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/02_2024/8ext_28662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/02_2024/8ext_28662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/02_2024/8ext_28662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/02_2024/8ext_28662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/02_2024/8ext_28662.pdb" } resolution = 4.6 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= 0.003 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 5806 2.51 5 N 1460 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "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 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 552": "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 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 552": "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: 8846 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4422 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 520} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4422 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 520} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} Time building chain proxies: 4.99, per 1000 atoms: 0.56 Number of scatterers: 8846 At special positions: 0 Unit cell: (88.395, 92.655, 116.085, 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 1540 8.00 N 1460 7.00 C 5806 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 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 " 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 60.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 1 through 31 Processing helix chain 'A' and resid 36 through 48 removed outlier: 4.044A pdb=" N TYR A 40 " --> pdb=" O TYR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.846A pdb=" N ASP A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 removed outlier: 5.172A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 193 through 208 Processing helix chain 'A' and resid 209 through 225 Processing helix chain 'A' and resid 228 through 252 Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.808A pdb=" N LEU A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 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 390 Processing helix chain 'A' and resid 391 through 402 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 removed outlier: 3.530A pdb=" N THR A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.617A pdb=" N SER A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 36 through 48 removed outlier: 4.044A pdb=" N TYR B 40 " --> pdb=" O TYR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 99 through 134 removed outlier: 3.846A pdb=" N ASP B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 152 removed outlier: 5.173A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 193 through 208 Processing helix chain 'B' and resid 209 through 225 Processing helix chain 'B' and resid 228 through 252 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.808A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) 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 390 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 450 through 461 removed outlier: 3.530A pdb=" N THR B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.616A pdb=" N SER B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.645A pdb=" N VAL A 160 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG A 162 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.615A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 530 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY A 539 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A 528 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 541 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS A 526 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 543 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A 524 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 545 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 522 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 517 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 523 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.645A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 7.076A 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: 6.615A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY B 530 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B 539 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY B 528 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 541 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS B 526 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY B 543 " --> pdb=" O TYR B 524 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR B 524 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 545 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU B 522 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS B 517 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 523 " --> pdb=" O ILE B 515 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1461 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: 2.54 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1815 1.31 - 1.44: 2726 1.44 - 1.58: 4399 1.58 - 1.71: 38 1.71 - 1.84: 68 Bond restraints: 9046 Sorted by residual: bond pdb=" CB HIS A 282 " pdb=" CG HIS A 282 " ideal model delta sigma weight residual 1.497 1.335 0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CB HIS B 282 " pdb=" CG HIS B 282 " ideal model delta sigma weight residual 1.497 1.335 0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.349 0.148 1.40e-02 5.10e+03 1.11e+02 bond pdb=" CB HIS A 153 " pdb=" CG HIS A 153 " ideal model delta sigma weight residual 1.497 1.349 0.148 1.40e-02 5.10e+03 1.11e+02 bond pdb=" CB PHE A 220 " pdb=" CG PHE A 220 " ideal model delta sigma weight residual 1.502 1.312 0.190 2.30e-02 1.89e+03 6.83e+01 ... (remaining 9041 not shown) Histogram of bond angle deviations from ideal: 85.66 - 98.27: 6 98.27 - 110.88: 3084 110.88 - 123.50: 8590 123.50 - 136.11: 488 136.11 - 148.72: 4 Bond angle restraints: 12172 Sorted by residual: angle pdb=" O ASP B 346 " pdb=" C ASP B 346 " pdb=" N TYR B 347 " ideal model delta sigma weight residual 122.79 148.72 -25.93 1.14e+00 7.69e-01 5.17e+02 angle pdb=" O ASP A 346 " pdb=" C ASP A 346 " pdb=" N TYR A 347 " ideal model delta sigma weight residual 122.79 148.72 -25.93 1.14e+00 7.69e-01 5.17e+02 angle pdb=" CA ASP A 346 " pdb=" C ASP A 346 " pdb=" N TYR A 347 " ideal model delta sigma weight residual 115.27 85.66 29.61 1.34e+00 5.57e-01 4.88e+02 angle pdb=" CA ASP B 346 " pdb=" C ASP B 346 " pdb=" N TYR B 347 " ideal model delta sigma weight residual 115.27 85.66 29.61 1.34e+00 5.57e-01 4.88e+02 angle pdb=" O ILE A 51 " pdb=" C ILE A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 121.10 136.04 -14.94 1.14e+00 7.69e-01 1.72e+02 ... (remaining 12167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 5016 14.03 - 28.05: 308 28.05 - 42.08: 70 42.08 - 56.10: 28 56.10 - 70.13: 10 Dihedral angle restraints: 5432 sinusoidal: 2256 harmonic: 3176 Sorted by residual: dihedral pdb=" C LEU B 18 " pdb=" N LEU B 18 " pdb=" CA LEU B 18 " pdb=" CB LEU B 18 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C LEU A 18 " pdb=" N LEU A 18 " pdb=" CA LEU A 18 " pdb=" CB LEU A 18 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C ASN B 406 " pdb=" N ASN B 406 " pdb=" CA ASN B 406 " pdb=" CB ASN B 406 " ideal model delta harmonic sigma weight residual -122.60 -132.21 9.61 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 716 0.085 - 0.171: 414 0.171 - 0.256: 156 0.256 - 0.341: 36 0.341 - 0.426: 14 Chirality restraints: 1336 Sorted by residual: chirality pdb=" CA TYR A 178 " pdb=" N TYR A 178 " pdb=" C TYR A 178 " pdb=" CB TYR A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA TYR B 178 " pdb=" N TYR B 178 " pdb=" C TYR B 178 " pdb=" CB TYR B 178 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA PHE B 151 " pdb=" N PHE B 151 " pdb=" C PHE B 151 " pdb=" CB PHE B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1333 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 346 " 0.022 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C ASP A 346 " -0.125 2.00e-02 2.50e+03 pdb=" O ASP A 346 " 0.058 2.00e-02 2.50e+03 pdb=" N TYR A 347 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 346 " -0.022 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C ASP B 346 " 0.125 2.00e-02 2.50e+03 pdb=" O ASP B 346 " -0.058 2.00e-02 2.50e+03 pdb=" N TYR B 347 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " 0.024 2.00e-02 2.50e+03 6.08e-02 3.70e+01 pdb=" C ILE A 51 " -0.105 2.00e-02 2.50e+03 pdb=" O ILE A 51 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO A 52 " 0.036 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 174 2.59 - 3.17: 9050 3.17 - 3.75: 15210 3.75 - 4.32: 22367 4.32 - 4.90: 32315 Nonbonded interactions: 79116 Sorted by model distance: nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.014 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.014 2.230 nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.021 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.022 2.230 nonbonded pdb=" O MET A 33 " pdb=" CD1 LEU B 311 " model vdw 2.281 3.460 ... (remaining 79111 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: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 2.130 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 28.320 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4877 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 : 0.026 0.190 9046 Z= 1.677 Angle : 2.042 29.611 12172 Z= 1.432 Chirality : 0.123 0.426 1336 Planarity : 0.010 0.073 1488 Dihedral : 10.968 70.129 3384 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.33 % Favored : 93.90 % Rotamer: Outliers : 2.03 % Allowed : 1.01 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1050 helix: -0.09 (0.19), residues: 550 sheet: -0.87 (0.47), residues: 118 loop : -0.57 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.011 TRP B 540 HIS 0.014 0.003 HIS B 213 PHE 0.045 0.006 PHE B 151 TYR 0.056 0.010 TYR B 203 ARG 0.004 0.001 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8475 (mt) cc_final: 0.8015 (mm) REVERT: A 20 LEU cc_start: 0.8877 (mt) cc_final: 0.8629 (mt) REVERT: A 37 LYS cc_start: 0.8324 (mttt) cc_final: 0.8005 (mttt) REVERT: A 119 PHE cc_start: 0.7232 (m-10) cc_final: 0.6999 (m-80) REVERT: A 260 THR cc_start: 0.7838 (t) cc_final: 0.7605 (t) REVERT: A 314 ILE cc_start: 0.8847 (mt) cc_final: 0.8631 (mt) REVERT: A 341 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5324 (tppt) outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.1952 time to fit residues: 39.7271 Evaluate side-chains 101 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.2980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS B 409 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 487 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4653 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9046 Z= 0.217 Angle : 0.722 7.318 12172 Z= 0.392 Chirality : 0.046 0.235 1336 Planarity : 0.005 0.047 1488 Dihedral : 5.376 19.625 1156 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 1.62 % Favored : 97.77 % 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 (0.25), residues: 1050 helix: 0.84 (0.20), residues: 584 sheet: -0.08 (0.49), residues: 120 loop : -0.68 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 39 HIS 0.015 0.002 HIS A 213 PHE 0.024 0.002 PHE A 248 TYR 0.037 0.002 TYR B 203 ARG 0.004 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 TYR cc_start: 0.6674 (p90) cc_final: 0.5742 (p90) REVERT: B 37 LYS cc_start: 0.8124 (mttt) cc_final: 0.7801 (mmtm) REVERT: B 152 ASN cc_start: 0.7067 (m-40) cc_final: 0.6618 (t0) REVERT: B 181 LEU cc_start: 0.7411 (mp) cc_final: 0.6934 (mp) REVERT: B 209 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7317 (mtt180) REVERT: B 216 ILE cc_start: 0.8122 (mt) cc_final: 0.7551 (mt) REVERT: B 218 ASN cc_start: 0.8581 (m110) cc_final: 0.8185 (m110) REVERT: B 221 SER cc_start: 0.8294 (m) cc_final: 0.8019 (p) REVERT: B 235 ARG cc_start: 0.5804 (mmt180) cc_final: 0.5521 (mmm160) REVERT: B 316 ILE cc_start: 0.7482 (tp) cc_final: 0.7251 (tp) outliers start: 3 outliers final: 0 residues processed: 137 average time/residue: 0.1667 time to fit residues: 28.7944 Evaluate side-chains 107 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 overall best weight: 1.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN B 428 GLN B 497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4695 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9046 Z= 0.180 Angle : 0.615 7.881 12172 Z= 0.333 Chirality : 0.042 0.145 1336 Planarity : 0.004 0.031 1488 Dihedral : 5.034 20.201 1156 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.61 % Allowed : 2.64 % Favored : 96.75 % 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 (0.25), residues: 1050 helix: 0.39 (0.20), residues: 592 sheet: 0.07 (0.53), residues: 112 loop : -1.15 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 475 HIS 0.015 0.002 HIS A 239 PHE 0.012 0.002 PHE A 16 TYR 0.036 0.002 TYR B 203 ARG 0.003 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3418 (ttt) cc_final: 0.1466 (mmt) REVERT: B 152 ASN cc_start: 0.7189 (m-40) cc_final: 0.6738 (t0) REVERT: B 179 ILE cc_start: 0.7385 (mt) cc_final: 0.6883 (mt) REVERT: B 216 ILE cc_start: 0.8229 (mt) cc_final: 0.7906 (mt) REVERT: B 218 ASN cc_start: 0.8500 (m110) cc_final: 0.8158 (m-40) REVERT: B 287 LYS cc_start: 0.4042 (tptt) cc_final: 0.3731 (tptt) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.1681 time to fit residues: 26.6483 Evaluate side-chains 96 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS B 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4639 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9046 Z= 0.156 Angle : 0.586 6.620 12172 Z= 0.315 Chirality : 0.042 0.174 1336 Planarity : 0.004 0.032 1488 Dihedral : 4.763 18.914 1156 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.20 % Allowed : 2.43 % Favored : 97.36 % 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: -0.27 (0.26), residues: 1050 helix: 0.43 (0.20), residues: 598 sheet: -0.51 (0.51), residues: 120 loop : -0.99 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 475 HIS 0.011 0.002 HIS B 213 PHE 0.015 0.002 PHE B 319 TYR 0.032 0.001 TYR A 203 ARG 0.003 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3234 (ttt) cc_final: 0.1498 (mmt) REVERT: B 37 LYS cc_start: 0.8278 (mmtp) cc_final: 0.7871 (mmtm) REVERT: B 119 PHE cc_start: 0.7138 (m-10) cc_final: 0.6829 (m-80) REVERT: B 152 ASN cc_start: 0.7109 (m-40) cc_final: 0.6636 (t0) REVERT: B 209 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7836 (mtt180) REVERT: B 239 HIS cc_start: 0.5903 (m90) cc_final: 0.5608 (m-70) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1449 time to fit residues: 23.5766 Evaluate side-chains 98 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 87 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4603 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9046 Z= 0.147 Angle : 0.610 10.310 12172 Z= 0.323 Chirality : 0.042 0.168 1336 Planarity : 0.004 0.034 1488 Dihedral : 4.571 17.575 1156 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1050 helix: 0.49 (0.20), residues: 604 sheet: -0.73 (0.50), residues: 120 loop : -1.17 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 475 HIS 0.008 0.002 HIS A 239 PHE 0.012 0.001 PHE B 248 TYR 0.028 0.001 TYR B 203 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3369 (ttt) cc_final: 0.1697 (mmt) REVERT: B 119 PHE cc_start: 0.7001 (m-10) cc_final: 0.6669 (m-80) REVERT: B 152 ASN cc_start: 0.6983 (m-40) cc_final: 0.6654 (t0) REVERT: B 216 ILE cc_start: 0.8160 (mt) cc_final: 0.7822 (mt) REVERT: B 239 HIS cc_start: 0.6430 (m90) cc_final: 0.5988 (m-70) REVERT: B 240 ASP cc_start: 0.6828 (p0) cc_final: 0.6471 (p0) REVERT: B 249 VAL cc_start: 0.8313 (t) cc_final: 0.8044 (t) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1352 time to fit residues: 21.5383 Evaluate side-chains 96 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 8 optimal weight: 0.0980 chunk 33 optimal weight: 0.0770 chunk 53 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4576 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9046 Z= 0.142 Angle : 0.603 8.478 12172 Z= 0.319 Chirality : 0.043 0.172 1336 Planarity : 0.004 0.034 1488 Dihedral : 4.404 16.694 1156 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -0.48 (0.25), residues: 1050 helix: 0.36 (0.20), residues: 602 sheet: -0.67 (0.51), residues: 120 loop : -1.27 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 475 HIS 0.009 0.001 HIS A 239 PHE 0.023 0.001 PHE A 442 TYR 0.032 0.001 TYR A 203 ARG 0.003 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3610 (ttt) cc_final: 0.1769 (mmt) REVERT: B 119 PHE cc_start: 0.6951 (m-10) cc_final: 0.6653 (m-80) REVERT: B 152 ASN cc_start: 0.7083 (m-40) cc_final: 0.6599 (t0) REVERT: B 229 LEU cc_start: 0.7788 (tp) cc_final: 0.7269 (tp) REVERT: B 239 HIS cc_start: 0.6426 (m90) cc_final: 0.5935 (m-70) REVERT: B 240 ASP cc_start: 0.6652 (p0) cc_final: 0.6401 (p0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1329 time to fit residues: 20.4306 Evaluate side-chains 94 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 0.0040 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN B 282 HIS ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4582 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9046 Z= 0.141 Angle : 0.567 6.629 12172 Z= 0.308 Chirality : 0.043 0.166 1336 Planarity : 0.004 0.034 1488 Dihedral : 4.343 15.376 1156 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.41 (0.25), residues: 1050 helix: 0.51 (0.20), residues: 602 sheet: -0.81 (0.49), residues: 120 loop : -1.39 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 475 HIS 0.010 0.001 HIS A 239 PHE 0.030 0.001 PHE A 12 TYR 0.022 0.001 TYR B 203 ARG 0.002 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.6851 (tpm170) cc_final: 0.4502 (ttt-90) REVERT: B 119 PHE cc_start: 0.6922 (m-10) cc_final: 0.6631 (m-80) REVERT: B 152 ASN cc_start: 0.6926 (m-40) cc_final: 0.6635 (t0) REVERT: B 174 TRP cc_start: 0.2606 (t60) cc_final: 0.2295 (t60) REVERT: B 239 HIS cc_start: 0.6631 (m90) cc_final: 0.6011 (m-70) REVERT: B 249 VAL cc_start: 0.8340 (t) cc_final: 0.8102 (t) REVERT: B 412 MET cc_start: 0.0546 (ptm) cc_final: 0.0079 (mtm) REVERT: B 476 MET cc_start: 0.1785 (mmm) cc_final: -0.0298 (mtt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1458 time to fit residues: 22.8317 Evaluate side-chains 97 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4570 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9046 Z= 0.144 Angle : 0.565 7.848 12172 Z= 0.307 Chirality : 0.042 0.156 1336 Planarity : 0.004 0.034 1488 Dihedral : 4.213 15.697 1156 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1050 helix: 0.60 (0.21), residues: 602 sheet: -0.62 (0.51), residues: 112 loop : -1.47 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 475 HIS 0.009 0.001 HIS B 213 PHE 0.011 0.001 PHE A 248 TYR 0.018 0.001 TYR B 203 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3943 (ttt) cc_final: 0.1868 (mmt) REVERT: B 28 ARG cc_start: 0.6917 (tpm170) cc_final: 0.4641 (ttt-90) REVERT: B 119 PHE cc_start: 0.6852 (m-10) cc_final: 0.6606 (m-80) REVERT: B 152 ASN cc_start: 0.6996 (m-40) cc_final: 0.6618 (t0) REVERT: B 174 TRP cc_start: 0.2543 (t60) cc_final: 0.2185 (t60) REVERT: B 239 HIS cc_start: 0.6562 (m90) cc_final: 0.6037 (m-70) REVERT: B 240 ASP cc_start: 0.6487 (p0) cc_final: 0.6166 (p0) REVERT: B 249 VAL cc_start: 0.8458 (t) cc_final: 0.8054 (t) REVERT: B 476 MET cc_start: 0.2012 (mmm) cc_final: 0.0017 (mtm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1428 time to fit residues: 22.1121 Evaluate side-chains 96 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 0.0060 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.0040 chunk 90 optimal weight: 0.0770 chunk 94 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.1366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 ASN B 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4518 moved from start: 0.7793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9046 Z= 0.145 Angle : 0.568 10.751 12172 Z= 0.307 Chirality : 0.042 0.159 1336 Planarity : 0.004 0.033 1488 Dihedral : 4.168 15.156 1156 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.20 % Allowed : 0.61 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1050 helix: 0.43 (0.20), residues: 602 sheet: -0.51 (0.52), residues: 112 loop : -1.54 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 475 HIS 0.009 0.001 HIS B 213 PHE 0.028 0.001 PHE B 12 TYR 0.025 0.001 TYR B 394 ARG 0.002 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.3796 (ttt) cc_final: 0.1826 (mmt) REVERT: B 28 ARG cc_start: 0.6779 (tpm170) cc_final: 0.4388 (ttt-90) REVERT: B 119 PHE cc_start: 0.6822 (m-10) cc_final: 0.6494 (m-80) REVERT: B 152 ASN cc_start: 0.6853 (m-40) cc_final: 0.6481 (t0) REVERT: B 239 HIS cc_start: 0.6472 (m90) cc_final: 0.6099 (m-70) REVERT: B 240 ASP cc_start: 0.6482 (p0) cc_final: 0.6154 (p0) REVERT: B 476 MET cc_start: 0.1816 (mmm) cc_final: -0.0213 (mtm) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1299 time to fit residues: 20.9804 Evaluate side-chains 94 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.0170 chunk 89 optimal weight: 0.0030 overall best weight: 0.5428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4529 moved from start: 0.8122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9046 Z= 0.142 Angle : 0.569 6.663 12172 Z= 0.308 Chirality : 0.043 0.218 1336 Planarity : 0.003 0.033 1488 Dihedral : 4.133 15.266 1156 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.57 (0.25), residues: 1050 helix: 0.45 (0.20), residues: 602 sheet: -0.79 (0.51), residues: 112 loop : -1.64 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 475 HIS 0.008 0.001 HIS A 213 PHE 0.034 0.002 PHE B 220 TYR 0.018 0.001 TYR A 441 ARG 0.003 0.000 ARG A 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4011 (ttt) cc_final: 0.1860 (mmt) REVERT: A 28 ARG cc_start: 0.6896 (tpm170) cc_final: 0.4619 (ttt-90) REVERT: A 119 PHE cc_start: 0.6879 (m-10) cc_final: 0.6568 (m-80) REVERT: A 152 ASN cc_start: 0.6886 (m-40) cc_final: 0.6511 (t0) REVERT: A 154 GLN cc_start: 0.6096 (mm110) cc_final: 0.5779 (mm-40) REVERT: A 209 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7476 (mtt180) REVERT: A 239 HIS cc_start: 0.6345 (m90) cc_final: 0.6083 (m-70) REVERT: A 240 ASP cc_start: 0.6402 (p0) cc_final: 0.6149 (p0) REVERT: A 249 VAL cc_start: 0.8451 (t) cc_final: 0.8126 (t) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1368 time to fit residues: 20.2526 Evaluate side-chains 92 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.0070 chunk 12 optimal weight: 0.0970 chunk 23 optimal weight: 0.0030 chunk 84 optimal weight: 0.0770 chunk 35 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.0030 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.0374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.153959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.110356 restraints weight = 12885.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.114505 restraints weight = 8773.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.117273 restraints weight = 6464.598| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9046 Z= 0.150 Angle : 0.588 10.981 12172 Z= 0.312 Chirality : 0.043 0.157 1336 Planarity : 0.003 0.034 1488 Dihedral : 4.114 14.721 1156 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.61 (0.25), residues: 1050 helix: 0.35 (0.20), residues: 602 sheet: -0.69 (0.52), residues: 104 loop : -1.53 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 174 HIS 0.007 0.001 HIS A 213 PHE 0.024 0.001 PHE B 173 TYR 0.017 0.001 TYR B 178 ARG 0.003 0.000 ARG A 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1704.40 seconds wall clock time: 32 minutes 13.73 seconds (1933.73 seconds total)