Starting phenix.real_space_refine on Thu Jul 2 07:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d9t_30620/07_2026/7d9t_30620.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4784 2.51 5 N 1279 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7451 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3235 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 3232 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1075 Unresolved non-hydrogen dihedrals: 728 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'TYR:plan': 7, 'HIS:plan': 9, 'GLU:plan': 33, 'PHE:plan': 14, 'ARG:plan': 17, 'ASN:plan1': 7, 'GLN:plan1': 12, 'ASP:plan': 18} Unresolved non-hydrogen planarities: 518 Conformer: "B" Number of residues, atoms: 512, 3232 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1075 Unresolved non-hydrogen dihedrals: 728 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'TYR:plan': 7, 'HIS:plan': 9, 'GLU:plan': 33, 'PHE:plan': 14, 'ARG:plan': 17, 'ASN:plan1': 7, 'GLN:plan1': 12, 'ASP:plan': 18} Unresolved non-hydrogen planarities: 518 bond proxies already assigned to first conformer: 3276 Chain: "B" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 567, 4170 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543} Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 29, 'TYR:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 10, 'PHE:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 263 Conformer: "B" Number of residues, atoms: 567, 4170 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543} Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 29, 'TYR:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 10, 'PHE:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 263 bond proxies already assigned to first conformer: 4249 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z90': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 residue: pdb=" N GLU A 325 " occ=0.75 ... (3 atoms not shown) pdb=" CB GLU A 325 " occ=0.75 residue: pdb=" N MET A 341 " occ=0.75 ... (3 atoms not shown) pdb=" CB MET A 341 " occ=0.75 Time building chain proxies: 2.55, per 1000 atoms: 0.34 Number of scatterers: 7451 At special positions: 0 Unit cell: (149.435, 71.06, 100.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1353 8.00 N 1279 7.00 C 4784 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 - 3.00 Amino acid : True - 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: 0.77 Conformation dependent library (CDL) restraints added in 625.9 milliseconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 48.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 100 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.432A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 4.228A pdb=" N LEU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.584A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.642A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.091A pdb=" N GLY A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.679A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 561 removed outlier: 3.790A pdb=" N ASP A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.762A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.788A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.009A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 4.153A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.923A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.734A pdb=" N ILE B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 112 removed outlier: 4.580A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.848A pdb=" N ARG B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.796A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 359 through 395 removed outlier: 3.759A pdb=" N LEU B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 367 " --> pdb=" O TYR B 363 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 409 removed outlier: 3.969A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 439 through 461 Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.170A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.944A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 3.679A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 232 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.931A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 524 removed outlier: 4.529A pdb=" N ASN A 479 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY A 580 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 618 removed outlier: 4.299A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 124 Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.881A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.484A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.484A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 599 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 601 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 587 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512 469 hydrogen bonds defined for protein. 1343 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: 0.94 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2452 1.34 - 1.46: 1489 1.46 - 1.58: 3597 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7586 Sorted by residual: bond pdb=" CBN Z90 B 701 " pdb=" CBO Z90 B 701 " ideal model delta sigma weight residual 1.405 1.483 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CAX Z90 B 701 " pdb=" CBG Z90 B 701 " ideal model delta sigma weight residual 1.542 1.506 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CBE Z90 B 701 " pdb=" NBP Z90 B 701 " ideal model delta sigma weight residual 1.449 1.477 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" CBH Z90 B 701 " pdb=" CBM Z90 B 701 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CBB Z90 B 701 " pdb=" NBP Z90 B 701 " ideal model delta sigma weight residual 1.454 1.472 -0.018 2.00e-02 2.50e+03 7.91e-01 ... (remaining 7581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10212 1.79 - 3.58: 151 3.58 - 5.36: 19 5.36 - 7.15: 7 7.15 - 8.94: 1 Bond angle restraints: 10390 Sorted by residual: angle pdb=" N VAL A 155 " pdb=" CA VAL A 155 " pdb=" C VAL A 155 " ideal model delta sigma weight residual 111.88 108.21 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta sigma weight residual 121.54 127.61 -6.07 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" N VAL B 239 " pdb=" CA VAL B 239 " pdb=" C VAL B 239 " ideal model delta sigma weight residual 113.16 108.88 4.28 1.49e+00 4.50e-01 8.24e+00 angle pdb=" N LYS A 555 " pdb=" CA LYS A 555 " pdb=" C LYS A 555 " ideal model delta sigma weight residual 111.36 108.32 3.04 1.09e+00 8.42e-01 7.80e+00 ... (remaining 10385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.30: 4404 28.30 - 56.59: 69 56.59 - 84.89: 4 84.89 - 113.18: 1 113.18 - 141.48: 1 Dihedral angle restraints: 4479 sinusoidal: 1347 harmonic: 3132 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CAX Z90 B 701 " pdb=" CAV Z90 B 701 " pdb=" CAW Z90 B 701 " pdb=" CBB Z90 B 701 " ideal model delta sinusoidal sigma weight residual 179.41 37.93 141.48 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" CA LEU B 338 " pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 844 0.030 - 0.060: 302 0.060 - 0.090: 85 0.090 - 0.120: 59 0.120 - 0.149: 8 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CB THR A 511 " pdb=" CA THR A 511 " pdb=" OG1 THR A 511 " pdb=" CG2 THR A 511 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE A 528 " pdb=" N ILE A 528 " pdb=" C ILE A 528 " pdb=" CB ILE A 528 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE A 403 " pdb=" N ILE A 403 " pdb=" C ILE A 403 " pdb=" CB ILE A 403 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1295 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 554 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL A 554 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL A 554 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 555 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 4 " 0.007 2.00e-02 2.50e+03 8.69e-03 1.32e+00 pdb=" CG PHE B 4 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 4 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 4 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 4 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 4 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 458 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 459 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 459 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 459 " 0.015 5.00e-02 4.00e+02 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1366 2.76 - 3.30: 7435 3.30 - 3.83: 12064 3.83 - 4.37: 12847 4.37 - 4.90: 22726 Nonbonded interactions: 56438 Sorted by model distance: nonbonded pdb=" O VAL B 397 " pdb=" OH TYR B 470 " model vdw 2.230 3.040 nonbonded pdb=" NH2 ARG B 238 " pdb=" OD2 ASP B 342 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR B 454 " pdb=" O GLY B 476 " model vdw 2.296 3.040 nonbonded pdb=" O PHE B 223 " pdb=" OG SER B 318 " model vdw 2.308 3.040 nonbonded pdb=" NH1 ARG B 121 " pdb=" O SER B 270 " model vdw 2.310 3.120 ... (remaining 56433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 1.040 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7586 Z= 0.146 Angle : 0.567 8.938 10390 Z= 0.320 Chirality : 0.039 0.149 1298 Planarity : 0.003 0.026 1334 Dihedral : 10.987 141.481 2441 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.25), residues: 1052 helix: -0.27 (0.22), residues: 496 sheet: -1.81 (0.31), residues: 220 loop : -2.18 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.017 0.001 TYR A 399 PHE 0.019 0.001 PHE B 4 TRP 0.004 0.001 TRP A 467 HIS 0.001 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 ( 7586) covalent geometry : angle 0.56680 / 0.32 (10390) hydrogen bonds : bond 0.17201 / 12.56 ( 457) hydrogen bonds : angle 6.62449 / 4.72 ( 1343) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASN cc_start: 0.8093 (t0) cc_final: 0.7782 (t0) REVERT: A 321 GLU cc_start: 0.7944 (pm20) cc_final: 0.7084 (pm20) REVERT: A 333 GLN cc_start: 0.8954 (pt0) cc_final: 0.8561 (pt0) REVERT: A 455 CYS cc_start: 0.8621 (p) cc_final: 0.8380 (p) REVERT: A 524 LYS cc_start: 0.9199 (tttt) cc_final: 0.8983 (ttmt) REVERT: B 38 LEU cc_start: 0.8927 (tt) cc_final: 0.8496 (mp) REVERT: B 65 GLU cc_start: 0.8831 (tp30) cc_final: 0.8579 (tp30) REVERT: B 69 MET cc_start: 0.8682 (mtp) cc_final: 0.8144 (mtm) REVERT: B 96 GLU cc_start: 0.9008 (mp0) cc_final: 0.8645 (mp0) REVERT: B 406 LEU cc_start: 0.9541 (tp) cc_final: 0.9296 (tt) REVERT: B 473 GLU cc_start: 0.8071 (pp20) cc_final: 0.7823 (tp30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0652 time to fit residues: 9.2918 Evaluate side-chains 71 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 HIS ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.050329 restraints weight = 43048.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.051887 restraints weight = 23747.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053059 restraints weight = 15887.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.053872 restraints weight = 11664.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054276 restraints weight = 9266.431| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 19 (27 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7586 Z= 0.157 Angle : 0.576 8.147 10390 Z= 0.300 Chirality : 0.041 0.142 1298 Planarity : 0.004 0.042 1334 Dihedral : 6.340 139.276 1136 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.15 % Allowed : 4.12 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.26), residues: 1052 helix: 0.72 (0.23), residues: 513 sheet: -1.43 (0.33), residues: 213 loop : -1.78 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 306 TYR 0.016 0.002 TYR A 399 PHE 0.025 0.002 PHE A 162 TRP 0.006 0.001 TRP B 602 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 7586) covalent geometry : angle 0.57590 / 0.30 (10390) hydrogen bonds : bond 0.03927 / 2.84 ( 457) hydrogen bonds : angle 4.86036 / 3.50 ( 1343) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9244 (t) cc_final: 0.8588 (p) REVERT: B 69 MET cc_start: 0.8672 (mtp) cc_final: 0.8085 (mtm) REVERT: B 96 GLU cc_start: 0.8995 (mp0) cc_final: 0.8722 (mp0) REVERT: B 406 LEU cc_start: 0.9449 (tp) cc_final: 0.9249 (tt) REVERT: B 480 MET cc_start: 0.8938 (ttp) cc_final: 0.8255 (ttp) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.0502 time to fit residues: 6.5436 Evaluate side-chains 64 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 0.8980 chunk 86 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 34 optimal weight: 0.1980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS B 377 GLN B 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.051431 restraints weight = 42509.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.053138 restraints weight = 22930.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054302 restraints weight = 14924.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055200 restraints weight = 10896.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.055699 restraints weight = 8547.066| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 7586 Z= 0.105 Angle : 0.547 8.112 10390 Z= 0.279 Chirality : 0.041 0.160 1298 Planarity : 0.004 0.043 1334 Dihedral : 6.235 135.788 1136 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.27), residues: 1052 helix: 1.22 (0.23), residues: 507 sheet: -1.28 (0.32), residues: 223 loop : -1.48 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 349 TYR 0.018 0.001 TYR A 399 PHE 0.020 0.001 PHE A 162 TRP 0.006 0.001 TRP B 602 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7586) covalent geometry : angle 0.54660 / 0.28 (10390) hydrogen bonds : bond 0.03375 / 2.42 ( 457) hydrogen bonds : angle 4.47653 / 3.22 ( 1343) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9203 (t) cc_final: 0.8522 (p) REVERT: A 339 MET cc_start: 0.9464 (tpp) cc_final: 0.9234 (tpp) REVERT: B 65 GLU cc_start: 0.8715 (tp30) cc_final: 0.8340 (tp30) REVERT: B 69 MET cc_start: 0.8640 (mtp) cc_final: 0.8075 (mtm) REVERT: B 96 GLU cc_start: 0.8993 (mp0) cc_final: 0.8725 (mp0) REVERT: B 473 GLU cc_start: 0.8242 (tp30) cc_final: 0.7964 (tp30) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0437 time to fit residues: 5.8988 Evaluate side-chains 61 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** 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 = 0.3114 r_free = 0.3114 target = 0.061095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.049842 restraints weight = 70564.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.052225 restraints weight = 34779.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054037 restraints weight = 17986.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055148 restraints weight = 11202.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.055284 restraints weight = 8307.170| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7586 Z= 0.117 Angle : 0.546 8.601 10390 Z= 0.278 Chirality : 0.041 0.146 1298 Planarity : 0.004 0.038 1334 Dihedral : 6.246 137.060 1136 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.27), residues: 1052 helix: 1.46 (0.24), residues: 507 sheet: -1.06 (0.33), residues: 228 loop : -1.34 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.016 0.001 TYR B 339 PHE 0.015 0.001 PHE A 162 TRP 0.005 0.001 TRP B 22 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7586) covalent geometry : angle 0.54599 / 0.28 (10390) hydrogen bonds : bond 0.03246 / 2.34 ( 457) hydrogen bonds : angle 4.24080 / 3.05 ( 1343) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9178 (t) cc_final: 0.8584 (p) REVERT: A 339 MET cc_start: 0.9437 (tpp) cc_final: 0.9236 (tpp) REVERT: B 65 GLU cc_start: 0.8806 (tp30) cc_final: 0.8393 (tp30) REVERT: B 69 MET cc_start: 0.8663 (mtp) cc_final: 0.8139 (mtm) REVERT: B 96 GLU cc_start: 0.8969 (mp0) cc_final: 0.8760 (mp0) REVERT: B 473 GLU cc_start: 0.8249 (tp30) cc_final: 0.7946 (tp30) REVERT: B 480 MET cc_start: 0.8876 (ttp) cc_final: 0.8405 (ttp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0464 time to fit residues: 5.7480 Evaluate side-chains 62 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN B 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.051585 restraints weight = 56072.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.053526 restraints weight = 27748.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.054894 restraints weight = 17050.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.055874 restraints weight = 11926.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.056476 restraints weight = 9124.922| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7586 Z= 0.101 Angle : 0.536 8.563 10390 Z= 0.270 Chirality : 0.041 0.142 1298 Planarity : 0.004 0.028 1334 Dihedral : 6.206 135.398 1136 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 1052 helix: 1.80 (0.24), residues: 492 sheet: -0.84 (0.33), residues: 226 loop : -1.31 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.017 0.001 TYR A 399 PHE 0.024 0.001 PHE A 162 TRP 0.005 0.001 TRP B 602 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 7586) covalent geometry : angle 0.53636 / 0.27 (10390) hydrogen bonds : bond 0.03039 / 2.20 ( 457) hydrogen bonds : angle 4.06523 / 2.93 ( 1343) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 LEU cc_start: 0.9100 (tp) cc_final: 0.8870 (tt) REVERT: A 438 GLN cc_start: 0.8446 (pp30) cc_final: 0.8057 (pp30) REVERT: B 65 GLU cc_start: 0.8726 (tp30) cc_final: 0.8420 (tp30) REVERT: B 69 MET cc_start: 0.8659 (mtp) cc_final: 0.8140 (mtm) REVERT: B 96 GLU cc_start: 0.8972 (mp0) cc_final: 0.8626 (mp0) REVERT: B 424 PHE cc_start: 0.8271 (m-80) cc_final: 0.6595 (m-10) REVERT: B 473 GLU cc_start: 0.8258 (tp30) cc_final: 0.8007 (tp30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0427 time to fit residues: 5.6052 Evaluate side-chains 69 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.059898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.049155 restraints weight = 56012.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.050974 restraints weight = 28185.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.052256 restraints weight = 17699.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.053013 restraints weight = 12506.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.053786 restraints weight = 9895.719| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7586 Z= 0.186 Angle : 0.588 9.681 10390 Z= 0.303 Chirality : 0.042 0.152 1298 Planarity : 0.004 0.044 1334 Dihedral : 6.409 139.629 1136 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.27), residues: 1052 helix: 1.72 (0.24), residues: 503 sheet: -0.79 (0.34), residues: 226 loop : -1.15 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.028 0.002 TYR A 399 PHE 0.018 0.002 PHE B 424 TRP 0.006 0.001 TRP A 467 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 7586) covalent geometry : angle 0.58827 / 0.30 (10390) hydrogen bonds : bond 0.03463 / 2.49 ( 457) hydrogen bonds : angle 4.25488 / 3.06 ( 1343) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9203 (t) cc_final: 0.8598 (p) REVERT: A 339 MET cc_start: 0.9389 (tpp) cc_final: 0.9036 (tpp) REVERT: A 441 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8645 (tm-30) REVERT: B 96 GLU cc_start: 0.9002 (mp0) cc_final: 0.8776 (mp0) REVERT: B 422 ILE cc_start: 0.9672 (mp) cc_final: 0.9444 (tp) REVERT: B 424 PHE cc_start: 0.8423 (m-80) cc_final: 0.8027 (m-10) REVERT: B 473 GLU cc_start: 0.8352 (tp30) cc_final: 0.8078 (tp30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0422 time to fit residues: 5.0473 Evaluate side-chains 63 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** 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 = 0.3132 r_free = 0.3132 target = 0.061767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.049761 restraints weight = 83227.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.052024 restraints weight = 35150.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.053423 restraints weight = 20197.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.054602 restraints weight = 13987.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.055390 restraints weight = 10332.646| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7586 Z= 0.105 Angle : 0.551 9.449 10390 Z= 0.279 Chirality : 0.041 0.180 1298 Planarity : 0.003 0.027 1334 Dihedral : 6.328 137.251 1136 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.27), residues: 1052 helix: 1.93 (0.24), residues: 490 sheet: -0.71 (0.34), residues: 226 loop : -1.08 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 306 TYR 0.020 0.001 TYR A 399 PHE 0.029 0.001 PHE B 4 TRP 0.005 0.001 TRP B 602 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 7586) covalent geometry : angle 0.55072 / 0.28 (10390) hydrogen bonds : bond 0.03190 / 2.28 ( 457) hydrogen bonds : angle 4.10223 / 2.96 ( 1343) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLN cc_start: 0.8363 (pp30) cc_final: 0.8004 (pp30) REVERT: B 96 GLU cc_start: 0.8969 (mp0) cc_final: 0.8611 (mp0) REVERT: B 473 GLU cc_start: 0.8356 (tp30) cc_final: 0.8128 (tp30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0438 time to fit residues: 5.8080 Evaluate side-chains 63 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** 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 = 0.3123 r_free = 0.3123 target = 0.061486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.050681 restraints weight = 54231.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.052491 restraints weight = 27490.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.053828 restraints weight = 17512.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.054680 restraints weight = 12339.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055429 restraints weight = 9574.933| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7586 Z= 0.116 Angle : 0.562 9.824 10390 Z= 0.283 Chirality : 0.042 0.181 1298 Planarity : 0.004 0.028 1334 Dihedral : 6.345 138.109 1136 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.43 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.27), residues: 1052 helix: 1.92 (0.24), residues: 496 sheet: -0.60 (0.34), residues: 226 loop : -1.05 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.018 0.001 TYR A 399 PHE 0.021 0.001 PHE B 4 TRP 0.004 0.001 TRP A 467 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7586) covalent geometry : angle 0.56222 / 0.28 (10390) hydrogen bonds : bond 0.03216 / 2.30 ( 457) hydrogen bonds : angle 4.07660 / 2.94 ( 1343) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9102 (t) cc_final: 0.8508 (p) REVERT: A 441 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8652 (tm-30) REVERT: B 65 GLU cc_start: 0.8622 (tp30) cc_final: 0.8299 (tp30) REVERT: B 69 MET cc_start: 0.8672 (mtp) cc_final: 0.8104 (mtm) REVERT: B 96 GLU cc_start: 0.8996 (mp0) cc_final: 0.8639 (mp0) REVERT: B 473 GLU cc_start: 0.8301 (tp30) cc_final: 0.8069 (tp30) REVERT: B 480 MET cc_start: 0.9229 (tpp) cc_final: 0.8740 (tpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0379 time to fit residues: 4.6391 Evaluate side-chains 63 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 28 optimal weight: 0.0270 chunk 91 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** 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 = 0.3137 r_free = 0.3137 target = 0.062085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050747 restraints weight = 70757.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.053298 restraints weight = 34545.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055107 restraints weight = 17483.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.055622 restraints weight = 11045.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.055856 restraints weight = 9465.982| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7586 Z= 0.104 Angle : 0.550 9.811 10390 Z= 0.276 Chirality : 0.041 0.172 1298 Planarity : 0.004 0.029 1334 Dihedral : 6.340 137.438 1136 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 1052 helix: 2.00 (0.24), residues: 498 sheet: -0.56 (0.34), residues: 226 loop : -0.97 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.016 0.001 TYR A 399 PHE 0.019 0.001 PHE B 4 TRP 0.004 0.001 TRP B 22 HIS 0.003 0.000 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 7586) covalent geometry : angle 0.55043 / 0.28 (10390) hydrogen bonds : bond 0.03084 / 2.21 ( 457) hydrogen bonds : angle 3.99759 / 2.89 ( 1343) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9061 (t) cc_final: 0.8534 (p) REVERT: B 65 GLU cc_start: 0.8678 (tp30) cc_final: 0.8379 (tp30) REVERT: B 69 MET cc_start: 0.8703 (mtp) cc_final: 0.8105 (mtm) REVERT: B 96 GLU cc_start: 0.8968 (mp0) cc_final: 0.8659 (mp0) REVERT: B 473 GLU cc_start: 0.8298 (tp30) cc_final: 0.8093 (tp30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0502 time to fit residues: 6.3404 Evaluate side-chains 62 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 0.0370 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 0.0670 chunk 12 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.051063 restraints weight = 97362.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.054054 restraints weight = 39369.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055703 restraints weight = 19275.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057027 restraints weight = 12074.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057205 restraints weight = 8914.545| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 7586 Z= 0.096 Angle : 0.544 9.344 10390 Z= 0.270 Chirality : 0.041 0.160 1298 Planarity : 0.003 0.030 1334 Dihedral : 6.290 136.712 1136 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.27), residues: 1052 helix: 2.00 (0.24), residues: 498 sheet: -0.46 (0.34), residues: 226 loop : -0.93 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.012 0.001 TYR A 399 PHE 0.020 0.001 PHE B 4 TRP 0.005 0.001 TRP B 602 HIS 0.002 0.000 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 7586) covalent geometry : angle 0.54426 / 0.27 (10390) hydrogen bonds : bond 0.02929 / 2.10 ( 457) hydrogen bonds : angle 3.91425 / 2.83 ( 1343) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9031 (t) cc_final: 0.8561 (p) REVERT: B 65 GLU cc_start: 0.8635 (tp30) cc_final: 0.8352 (tp30) REVERT: B 69 MET cc_start: 0.8702 (mtp) cc_final: 0.8097 (mtm) REVERT: B 96 GLU cc_start: 0.8944 (mp0) cc_final: 0.8665 (mp0) REVERT: B 473 GLU cc_start: 0.8295 (tp30) cc_final: 0.8050 (tp30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0458 time to fit residues: 5.6048 Evaluate side-chains 64 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 0.0570 chunk 66 optimal weight: 0.0060 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.051038 restraints weight = 97518.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.053391 restraints weight = 39274.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054976 restraints weight = 22202.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.056158 restraints weight = 14893.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056782 restraints weight = 10926.929| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 7586 Z= 0.096 Angle : 0.543 9.319 10390 Z= 0.270 Chirality : 0.041 0.158 1298 Planarity : 0.003 0.028 1334 Dihedral : 6.268 136.671 1136 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.27), residues: 1052 helix: 2.08 (0.24), residues: 498 sheet: -0.28 (0.35), residues: 220 loop : -0.88 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 306 TYR 0.011 0.001 TYR B 339 PHE 0.028 0.001 PHE B 4 TRP 0.005 0.001 TRP B 22 HIS 0.002 0.000 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 7586) covalent geometry : angle 0.54262 / 0.27 (10390) hydrogen bonds : bond 0.02897 / 2.07 ( 457) hydrogen bonds : angle 3.88218 / 2.81 ( 1343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 980.36 seconds wall clock time: 17 minutes 35.56 seconds (1055.56 seconds total)