Starting phenix.real_space_refine on Tue Feb 20 13:37:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zub_14971/02_2024/7zub_14971_trim_updated.pdb" } resolution = 2.85 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: 8 Type Number sf(0) Gaussians Mo 2 10.26 5 P 4 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 8887 2.51 5 N 2386 2.21 5 O 2698 1.98 5 H 14035 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28082 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 624, 10143 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 17, 'TRANS': 606} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 624, 10143 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 17, 'TRANS': 606} Chain breaks: 1 bond proxies already assigned to first conformer: 10195 Chain: "B" Number of atoms: 10357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 637, 10333 Classifications: {'peptide': 637} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 619} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 637, 10333 Classifications: {'peptide': 637} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 619} Chain breaks: 2 bond proxies already assigned to first conformer: 10391 Chain: "C" Number of atoms: 4914 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 304, 4875 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 14, 'TRANS': 289} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 304, 4875 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 14, 'TRANS': 289} Chain breaks: 1 bond proxies already assigned to first conformer: 4881 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2554 Classifications: {'peptide': 157} Modifications used: {'ACID-GLU': 1} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'MOO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'MOO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'JY6': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 612 " occ=0.44 ... (46 atoms not shown) pdb="HH22BARG B 612 " occ=0.56 residue: pdb=" N ASER C 256 " occ=0.64 ... (20 atoms not shown) pdb=" HG BSER C 256 " occ=0.36 residue: pdb=" O1 MOO B1003 " occ=0.98 ... (3 atoms not shown) pdb="MO MOO B1003 " occ=0.98 Time building chain proxies: 20.78, per 1000 atoms: 0.74 Number of scatterers: 28082 At special positions: 0 Unit cell: (130.32, 122.718, 148.782, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 2 41.97 S 68 16.00 P 4 15.00 Mg 2 11.99 O 2698 8.00 N 2386 7.00 C 8887 6.00 H 14035 1.00 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 Atom "HETATM28051 O3A ADP B1001 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.74 Conformation dependent library (CDL) restraints added in 5.0 seconds 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 10 sheets defined 41.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 36 through 59 removed outlier: 3.857A pdb=" N PHE A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 398 through 419 Processing helix chain 'A' and resid 424 through 443 removed outlier: 6.516A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.711A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.864A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 570 removed outlier: 5.251A pdb=" N ASN A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.611A pdb=" N ALA A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 649 through 666 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 36 through 59 removed outlier: 3.964A pdb=" N PHE B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 398 through 420 Processing helix chain 'B' and resid 423 through 443 removed outlier: 3.670A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.633A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 516 through 524 Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 561 through 570 Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.753A pdb=" N MET B 617 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY B 618 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 Processing helix chain 'B' and resid 649 through 665 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.689A pdb=" N ARG C 9 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 98 through 102 removed outlier: 4.241A pdb=" N ALA C 102 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 172 through 192 removed outlier: 4.044A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Proline residue: C 180 - end of helix Processing helix chain 'C' and resid 196 through 215 removed outlier: 3.591A pdb=" N MET C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 215 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 243 removed outlier: 3.679A pdb=" N GLN C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 247 through 260 removed outlier: 3.675A pdb=" N ASP C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 260 " --> pdb=" O ASER C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.589A pdb=" N ALA C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 324 Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.614A pdb=" N ILE D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 removed outlier: 3.950A pdb=" N CYS D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 343 removed outlier: 4.572A pdb=" N LEU D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 411 through 414 No H-bonds generated for 'chain 'D' and resid 411 through 414' Processing sheet with id= A, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.988A pdb=" N HIS A 184 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL A 143 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 182 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 145 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS A 180 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR A 147 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY A 178 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE A 75 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 214 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR A 216 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 317 through 322 removed outlier: 3.703A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 363 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.144A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 578 through 580 removed outlier: 8.783A pdb=" N THR A 579 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 626 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 276 through 280 removed outlier: 3.625A pdb=" N TYR B 276 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.703A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 354 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 532 through 535 removed outlier: 6.360A pdb=" N VAL B 511 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 577 through 580 removed outlier: 3.963A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 14 through 19 removed outlier: 4.278A pdb=" N GLN C 14 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU C 89 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 16 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 87 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 85 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR C 35 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL C 157 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS C 33 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS C 42 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 49 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 286 through 291 565 hydrogen bonds defined for protein. 1333 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: 9.79 Time building geometry restraints manager: 21.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.23: 14045 1.23 - 1.63: 14173 1.63 - 2.04: 122 2.04 - 2.45: 0 2.45 - 2.85: 1 Bond restraints: 28341 Sorted by residual: bond pdb=" OE2 GLU D 393 " pdb=" HE2 GLU D 393 " ideal model delta sigma weight residual 0.948 2.854 -1.906 2.00e-02 2.50e+03 9.08e+03 bond pdb=" O1 MOO A1003 " pdb="MO MOO A1003 " ideal model delta sigma weight residual 1.694 1.858 -0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" O1 MOO B1003 " pdb="MO MOO B1003 " ideal model delta sigma weight residual 1.694 1.857 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" O3 MOO B1003 " pdb="MO MOO B1003 " ideal model delta sigma weight residual 1.698 1.855 -0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" O3 MOO A1003 " pdb="MO MOO A1003 " ideal model delta sigma weight residual 1.698 1.855 -0.157 2.00e-02 2.50e+03 6.15e+01 ... (remaining 28336 not shown) Histogram of bond angle deviations from ideal: 15.34 - 40.40: 1 40.40 - 65.47: 0 65.47 - 90.54: 17 90.54 - 115.60: 36905 115.60 - 140.67: 14421 Bond angle restraints: 51344 Sorted by residual: angle pdb=" CD GLU D 393 " pdb=" OE2 GLU D 393 " pdb=" HE2 GLU D 393 " ideal model delta sigma weight residual 108.32 15.34 92.98 3.00e+00 1.11e-01 9.61e+02 angle pdb=" CG GLU D 393 " pdb=" CB GLU D 393 " pdb=" HB3 GLU D 393 " ideal model delta sigma weight residual 108.00 65.81 42.19 3.00e+00 1.11e-01 1.98e+02 angle pdb=" HB2 GLU D 393 " pdb=" CB GLU D 393 " pdb=" HB3 GLU D 393 " ideal model delta sigma weight residual 110.00 140.67 -30.67 3.00e+00 1.11e-01 1.05e+02 angle pdb=" HZ1 LYS C 103 " pdb=" NZ LYS C 103 " pdb=" HZ2 LYS C 103 " ideal model delta sigma weight residual 109.00 79.25 29.75 3.00e+00 1.11e-01 9.83e+01 angle pdb=" HZ1 LYS D 283 " pdb=" NZ LYS D 283 " pdb=" HZ2 LYS D 283 " ideal model delta sigma weight residual 109.00 79.28 29.72 3.00e+00 1.11e-01 9.82e+01 ... (remaining 51339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 12426 27.42 - 54.84: 679 54.84 - 82.25: 79 82.25 - 109.67: 12 109.67 - 137.09: 3 Dihedral angle restraints: 13199 sinusoidal: 7314 harmonic: 5885 Sorted by residual: dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 162.91 137.09 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 71.31 -131.31 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PB ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.35 116.35 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 13196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1609 0.039 - 0.077: 368 0.077 - 0.116: 117 0.116 - 0.155: 32 0.155 - 0.193: 1 Chirality restraints: 2127 Sorted by residual: chirality pdb=" CA MET B 394 " pdb=" N MET B 394 " pdb=" C MET B 394 " pdb=" CB MET B 394 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA ILE B 175 " pdb=" N ILE B 175 " pdb=" C ILE B 175 " pdb=" CB ILE B 175 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ARG C 325 " pdb=" N ARG C 325 " pdb=" C ARG C 325 " pdb=" CB ARG C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2124 not shown) Planarity restraints: 4136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N JY6 D1001 " -0.036 2.00e-02 2.50e+03 7.77e-02 3.02e+02 pdb=" C JY6 D1001 " -0.078 2.00e-02 2.50e+03 pdb=" O JY6 D1001 " 0.191 2.00e-02 2.50e+03 pdb=" C1 JY6 D1001 " -0.099 2.00e-02 2.50e+03 pdb=" C10 JY6 D1001 " 0.047 2.00e-02 2.50e+03 pdb=" C11 JY6 D1001 " -0.035 2.00e-02 2.50e+03 pdb=" C12 JY6 D1001 " -0.119 2.00e-02 2.50e+03 pdb=" C13 JY6 D1001 " -0.119 2.00e-02 2.50e+03 pdb=" C14 JY6 D1001 " -0.038 2.00e-02 2.50e+03 pdb=" C15 JY6 D1001 " 0.055 2.00e-02 2.50e+03 pdb=" C2 JY6 D1001 " -0.070 2.00e-02 2.50e+03 pdb=" C3 JY6 D1001 " -0.018 2.00e-02 2.50e+03 pdb=" C4 JY6 D1001 " 0.006 2.00e-02 2.50e+03 pdb=" C5 JY6 D1001 " -0.025 2.00e-02 2.50e+03 pdb=" C6 JY6 D1001 " 0.052 2.00e-02 2.50e+03 pdb=" C7 JY6 D1001 " 0.039 2.00e-02 2.50e+03 pdb=" C8 JY6 D1001 " 0.096 2.00e-02 2.50e+03 pdb=" C9 JY6 D1001 " 0.045 2.00e-02 2.50e+03 pdb=" N1 JY6 D1001 " 0.010 2.00e-02 2.50e+03 pdb=" O1 JY6 D1001 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 393 " -0.074 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" CD GLU D 393 " -0.055 2.00e-02 2.50e+03 pdb=" OE1 GLU D 393 " -0.216 2.00e-02 2.50e+03 pdb=" OE2 GLU D 393 " 0.122 2.00e-02 2.50e+03 pdb=" HE2 GLU D 393 " 0.223 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 196 " 0.217 9.50e-02 1.11e+02 7.24e-02 5.83e+00 pdb=" NE ARG B 196 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 196 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 196 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 196 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 196 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG B 196 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG B 196 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG B 196 " 0.005 2.00e-02 2.50e+03 ... (remaining 4133 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 70 1.80 - 2.50: 21353 2.50 - 3.20: 84343 3.20 - 3.90: 109451 3.90 - 4.60: 173428 Nonbonded interactions: 388645 Sorted by model distance: nonbonded pdb=" OE1 GLU D 393 " pdb=" HE2 GLU D 393 " model vdw 1.105 1.960 nonbonded pdb=" OE1 GLU A 173 " pdb=" H GLU A 173 " model vdw 1.410 1.850 nonbonded pdb=" OE1 GLN A 326 " pdb=" H GLN A 326 " model vdw 1.509 1.850 nonbonded pdb=" O THR C 32 " pdb=" H ILE C 64 " model vdw 1.521 1.850 nonbonded pdb=" OE1 GLU B 173 " pdb=" H GLU B 173 " model vdw 1.548 1.850 ... (remaining 388640 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' and (resid 11 through 34 or resid 36 through 319 or (resid 320 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1)) or resid 321 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 o \ r name HE1 or name HE2)) or resid 459 through 501 or resid 503 through 611 or re \ sid 613 through 690 or resid 1001 through 1003)) selection = (chain 'B' and (resid 11 through 34 or resid 36 through 219 or resid 276 through \ 501 or resid 503 through 611 or resid 613 through 690 or resid 1001 through 100 \ 3)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.36 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.400 Extract box with map and model: 8.010 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 95.540 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.005 0.164 14304 Z= 0.331 Angle : 0.563 11.663 19283 Z= 0.287 Chirality : 0.039 0.193 2127 Planarity : 0.004 0.091 2470 Dihedral : 17.292 137.088 5508 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.10 % Allowed : 18.42 % Favored : 80.48 % 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: 0.60 (0.21), residues: 1717 helix: 2.05 (0.20), residues: 699 sheet: 0.44 (0.30), residues: 292 loop : -1.33 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.004 0.001 HIS C 151 PHE 0.020 0.001 PHE C 68 TYR 0.010 0.001 TYR A 134 ARG 0.007 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 258 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7612 (mm) outliers start: 15 outliers final: 11 residues processed: 156 average time/residue: 2.9356 time to fit residues: 502.5484 Evaluate side-chains 140 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 406 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 68 optimal weight: 0.0970 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14304 Z= 0.179 Angle : 0.532 11.926 19283 Z= 0.280 Chirality : 0.039 0.154 2127 Planarity : 0.005 0.068 2470 Dihedral : 6.976 102.978 1927 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.30 % Allowed : 18.35 % Favored : 80.35 % 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: 0.22 (0.20), residues: 1717 helix: 1.40 (0.20), residues: 705 sheet: 0.66 (0.30), residues: 283 loop : -1.37 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 157 HIS 0.004 0.001 HIS C 94 PHE 0.018 0.001 PHE C 150 TYR 0.011 0.001 TYR A 134 ARG 0.009 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 2.246 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: C 258 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7593 (mm) REVERT: C 264 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6401 (t0) outliers start: 17 outliers final: 10 residues processed: 148 average time/residue: 2.8606 time to fit residues: 465.2811 Evaluate side-chains 139 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14304 Z= 0.301 Angle : 0.561 11.858 19283 Z= 0.293 Chirality : 0.041 0.145 2127 Planarity : 0.005 0.067 2470 Dihedral : 6.595 116.060 1917 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.82 % Allowed : 18.42 % Favored : 79.77 % 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: -0.12 (0.20), residues: 1717 helix: 1.02 (0.20), residues: 707 sheet: 0.52 (0.30), residues: 290 loop : -1.46 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 157 HIS 0.006 0.001 HIS B 320 PHE 0.020 0.002 PHE C 68 TYR 0.015 0.002 TYR A 134 ARG 0.011 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 2.245 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: B 194 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: C 258 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7587 (mm) outliers start: 25 outliers final: 12 residues processed: 147 average time/residue: 2.8089 time to fit residues: 453.6913 Evaluate side-chains 135 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14304 Z= 0.247 Angle : 0.539 11.684 19283 Z= 0.279 Chirality : 0.040 0.142 2127 Planarity : 0.005 0.073 2470 Dihedral : 6.565 122.247 1917 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.88 % Allowed : 18.55 % Favored : 79.57 % 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: -0.11 (0.20), residues: 1717 helix: 1.02 (0.20), residues: 705 sheet: 0.46 (0.30), residues: 289 loop : -1.41 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 157 HIS 0.007 0.001 HIS C 151 PHE 0.017 0.001 PHE C 68 TYR 0.013 0.001 TYR A 134 ARG 0.011 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 2.220 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: C 258 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7587 (mm) REVERT: C 264 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6334 (t0) REVERT: D 273 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7783 (mm-40) REVERT: D 361 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8562 (t) outliers start: 27 outliers final: 16 residues processed: 153 average time/residue: 2.7537 time to fit residues: 463.8749 Evaluate side-chains 138 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14304 Z= 0.194 Angle : 0.516 11.736 19283 Z= 0.266 Chirality : 0.039 0.142 2127 Planarity : 0.004 0.080 2470 Dihedral : 6.239 108.372 1917 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.01 % Allowed : 18.48 % Favored : 79.51 % 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 (0.21), residues: 1717 helix: 1.12 (0.21), residues: 702 sheet: 0.53 (0.30), residues: 289 loop : -1.37 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 157 HIS 0.007 0.001 HIS C 151 PHE 0.015 0.001 PHE C 68 TYR 0.012 0.001 TYR A 134 ARG 0.014 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 2.248 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: symmetry clash REVERT: A 545 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6779 (pp20) REVERT: B 194 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: B 196 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7240 (mtp-110) REVERT: C 91 ASP cc_start: 0.2571 (OUTLIER) cc_final: 0.2134 (m-30) REVERT: C 258 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7566 (mm) REVERT: C 264 ASN cc_start: 0.6642 (OUTLIER) cc_final: 0.6313 (t0) REVERT: D 273 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7767 (mm-40) REVERT: D 361 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8497 (t) outliers start: 29 outliers final: 17 residues processed: 153 average time/residue: 2.6729 time to fit residues: 452.3057 Evaluate side-chains 146 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14304 Z= 0.219 Angle : 0.526 11.662 19283 Z= 0.271 Chirality : 0.039 0.141 2127 Planarity : 0.004 0.067 2470 Dihedral : 6.232 112.902 1917 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.75 % Allowed : 19.07 % Favored : 79.18 % 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: -0.02 (0.21), residues: 1717 helix: 1.12 (0.21), residues: 701 sheet: 0.51 (0.30), residues: 289 loop : -1.37 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 157 HIS 0.007 0.001 HIS C 151 PHE 0.016 0.001 PHE C 68 TYR 0.012 0.001 TYR A 134 ARG 0.011 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 2.491 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: B 194 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: C 91 ASP cc_start: 0.2631 (OUTLIER) cc_final: 0.2211 (m-30) REVERT: C 258 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7567 (mm) REVERT: C 264 ASN cc_start: 0.6646 (OUTLIER) cc_final: 0.6336 (t0) REVERT: D 273 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7717 (mm-40) outliers start: 25 outliers final: 16 residues processed: 144 average time/residue: 2.6177 time to fit residues: 416.6264 Evaluate side-chains 142 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14304 Z= 0.190 Angle : 0.514 11.671 19283 Z= 0.263 Chirality : 0.039 0.141 2127 Planarity : 0.004 0.086 2470 Dihedral : 6.114 106.121 1917 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.82 % Allowed : 18.94 % Favored : 79.25 % 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: 0.03 (0.21), residues: 1717 helix: 1.17 (0.21), residues: 701 sheet: 0.52 (0.30), residues: 289 loop : -1.36 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 157 HIS 0.003 0.001 HIS B 320 PHE 0.015 0.001 PHE C 68 TYR 0.011 0.001 TYR A 134 ARG 0.015 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: B 196 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7160 (mtp-110) REVERT: C 91 ASP cc_start: 0.2734 (OUTLIER) cc_final: 0.2284 (m-30) REVERT: C 258 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7546 (mm) REVERT: C 264 ASN cc_start: 0.6596 (OUTLIER) cc_final: 0.6331 (t0) REVERT: D 273 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7736 (mm-40) REVERT: D 361 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8485 (t) REVERT: D 407 THR cc_start: 0.6142 (OUTLIER) cc_final: 0.5683 (p) outliers start: 26 outliers final: 16 residues processed: 146 average time/residue: 2.5763 time to fit residues: 416.7133 Evaluate side-chains 146 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 407 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14304 Z= 0.200 Angle : 0.517 11.768 19283 Z= 0.265 Chirality : 0.039 0.141 2127 Planarity : 0.004 0.074 2470 Dihedral : 6.018 108.104 1915 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.88 % Allowed : 18.94 % Favored : 79.18 % 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: 0.02 (0.21), residues: 1717 helix: 1.10 (0.21), residues: 713 sheet: 0.55 (0.30), residues: 288 loop : -1.35 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 157 HIS 0.004 0.001 HIS C 151 PHE 0.018 0.001 PHE C 68 TYR 0.012 0.001 TYR A 134 ARG 0.013 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 91 ASP cc_start: 0.2930 (OUTLIER) cc_final: 0.2495 (m-30) REVERT: C 258 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7548 (mm) REVERT: C 264 ASN cc_start: 0.6697 (OUTLIER) cc_final: 0.6402 (t0) REVERT: D 273 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7756 (mm-40) REVERT: D 361 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8490 (t) REVERT: D 407 THR cc_start: 0.6108 (OUTLIER) cc_final: 0.5647 (p) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 2.5346 time to fit residues: 416.8504 Evaluate side-chains 146 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 407 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14304 Z= 0.212 Angle : 0.521 11.794 19283 Z= 0.267 Chirality : 0.039 0.140 2127 Planarity : 0.005 0.091 2470 Dihedral : 6.037 109.486 1915 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.82 % Allowed : 19.20 % Favored : 78.99 % 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: -0.01 (0.21), residues: 1717 helix: 1.08 (0.21), residues: 714 sheet: 0.53 (0.30), residues: 288 loop : -1.36 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 157 HIS 0.004 0.001 HIS B 320 PHE 0.017 0.001 PHE C 68 TYR 0.012 0.001 TYR A 134 ARG 0.015 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 91 ASP cc_start: 0.2948 (OUTLIER) cc_final: 0.2506 (m-30) REVERT: C 258 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7516 (mm) REVERT: D 361 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8485 (t) REVERT: D 407 THR cc_start: 0.5827 (OUTLIER) cc_final: 0.5390 (p) outliers start: 26 outliers final: 16 residues processed: 144 average time/residue: 2.5308 time to fit residues: 403.9032 Evaluate side-chains 144 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 112 optimal weight: 0.0970 chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14304 Z= 0.167 Angle : 0.506 11.775 19283 Z= 0.258 Chirality : 0.039 0.142 2127 Planarity : 0.004 0.076 2470 Dihedral : 5.812 99.530 1915 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.43 % Allowed : 19.78 % Favored : 78.79 % 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: 0.12 (0.21), residues: 1717 helix: 1.21 (0.21), residues: 710 sheet: 0.59 (0.30), residues: 288 loop : -1.30 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 157 HIS 0.003 0.001 HIS C 151 PHE 0.014 0.001 PHE C 68 TYR 0.010 0.001 TYR B 134 ARG 0.015 0.000 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: C 91 ASP cc_start: 0.2949 (OUTLIER) cc_final: 0.2522 (m-30) REVERT: C 258 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7496 (mm) REVERT: D 361 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8486 (t) REVERT: D 407 THR cc_start: 0.5825 (OUTLIER) cc_final: 0.5378 (p) outliers start: 20 outliers final: 15 residues processed: 141 average time/residue: 2.6921 time to fit residues: 425.1304 Evaluate side-chains 143 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 407 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 138 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.086183 restraints weight = 87365.593| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.45 r_work: 0.2850 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14304 Z= 0.195 Angle : 0.518 11.807 19283 Z= 0.265 Chirality : 0.039 0.141 2127 Planarity : 0.005 0.109 2470 Dihedral : 5.890 104.535 1915 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.49 % Allowed : 19.84 % Favored : 78.66 % 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: 0.07 (0.21), residues: 1717 helix: 1.16 (0.21), residues: 715 sheet: 0.58 (0.30), residues: 288 loop : -1.34 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 157 HIS 0.004 0.001 HIS B 320 PHE 0.016 0.001 PHE C 68 TYR 0.011 0.001 TYR A 134 ARG 0.019 0.000 ARG B 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9190.13 seconds wall clock time: 161 minutes 41.38 seconds (9701.38 seconds total)