Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 23:10:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw6_24709/07_2023/7rw6_24709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw6_24709/07_2023/7rw6_24709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw6_24709/07_2023/7rw6_24709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw6_24709/07_2023/7rw6_24709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw6_24709/07_2023/7rw6_24709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw6_24709/07_2023/7rw6_24709.pdb" } resolution = 2.55 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 1.289 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 86 5.16 5 C 8388 2.51 5 N 2242 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 13130 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5100 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 24, 'TRANS': 617} Chain breaks: 4 Chain: "B" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1464 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Chain: "C" Number of atoms: 5100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5100 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 24, 'TRANS': 617} Chain breaks: 4 Chain: "D" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1464 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5776 SG CYS B 284 74.630 135.699 28.793 1.00 68.81 S ATOM 5817 SG CYS B 289 72.505 138.703 28.680 1.00 94.70 S ATOM 12340 SG CYS D 284 68.627 41.483 29.027 1.00 73.57 S ATOM 12381 SG CYS D 289 70.940 38.754 28.553 1.00 97.13 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N CYS B 344 " occ=0.62 ... (4 atoms not shown) pdb=" SG CYS B 344 " occ=0.62 residue: pdb=" N CYS B 354 " occ=0.56 ... (4 atoms not shown) pdb=" SG CYS B 354 " occ=0.56 residue: pdb=" N CYS D 344 " occ=0.62 ... (4 atoms not shown) pdb=" SG CYS D 344 " occ=0.62 residue: pdb=" N CYS D 354 " occ=0.56 ... (4 atoms not shown) pdb=" SG CYS D 354 " occ=0.56 Time building chain proxies: 7.19, per 1000 atoms: 0.55 Number of scatterers: 13130 At special positions: 0 Unit cell: (143.48, 178.084, 80.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 86 16.00 O 2412 8.00 N 2242 7.00 C 8388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 253 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 284 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 289 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 253 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 284 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 289 " 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 52.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 26 through 41 removed outlier: 3.615A pdb=" N ASP A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 31 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 115 through 135 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.991A pdb=" N PHE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.734A pdb=" N HIS A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.095A pdb=" N ALA A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 478 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 509 through 539 Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.729A pdb=" N GLY A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.724A pdb=" N VAL A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.853A pdb=" N GLN A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 661' Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 672 through 684 Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 706 through 718 Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 288 through 300 Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.693A pdb=" N VAL B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 379 removed outlier: 3.502A pdb=" N ASN B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.580A pdb=" N ASP C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 115 through 135 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 150 through 164 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 292 through 301 removed outlier: 3.827A pdb=" N PHE C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.779A pdb=" N HIS C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 422 through 426 removed outlier: 3.695A pdb=" N ALA C 426 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 4.183A pdb=" N ALA C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 478 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 495 through 503 Processing helix chain 'C' and resid 509 through 539 Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.722A pdb=" N GLY C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 583 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.809A pdb=" N GLN C 660 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 672 through 684 Processing helix chain 'C' and resid 685 through 687 No H-bonds generated for 'chain 'C' and resid 685 through 687' Processing helix chain 'C' and resid 706 through 718 Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 288 through 300 Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 361 through 379 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 169 removed outlier: 7.588A pdb=" N GLY A 490 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN A 404 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 492 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 406 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN A 494 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 408 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 removed outlier: 7.126A pdb=" N VAL A 256 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY A 288 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA A 258 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A 290 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET A 260 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 366 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR A 722 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 695 through 697 Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 230 removed outlier: 9.210A pdb=" N GLN B 332 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 305 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N SER B 334 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 307 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.579A pdb=" N GLY C 490 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN C 404 " --> pdb=" O GLY C 490 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLY C 492 " --> pdb=" O ASN C 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 406 " --> pdb=" O GLY C 492 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLN C 494 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE C 408 " --> pdb=" O GLN C 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.085A pdb=" N VAL C 256 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY C 288 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 258 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE C 290 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET C 260 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 366 " --> pdb=" O THR C 722 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR C 722 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 695 through 697 Processing sheet with id=AA9, first strand: chain 'D' and resid 227 through 230 Processing sheet with id=AB1, first strand: chain 'D' and resid 227 through 230 removed outlier: 9.178A pdb=" N GLN D 332 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU D 305 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER D 334 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE D 307 " --> pdb=" O SER D 334 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1767 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: 4.54 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4298 1.35 - 1.47: 3472 1.47 - 1.59: 5566 1.59 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 13458 Sorted by residual: bond pdb=" CA GLN B 352 " pdb=" CB GLN B 352 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.62e-02 3.81e+03 1.85e+00 bond pdb=" CA GLN D 352 " pdb=" CB GLN D 352 " ideal model delta sigma weight residual 1.529 1.550 -0.021 1.62e-02 3.81e+03 1.62e+00 bond pdb=" C LEU D 256 " pdb=" O LEU D 256 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.15e-02 7.56e+03 7.73e-01 bond pdb=" CG1 ILE A 16 " pdb=" CD1 ILE A 16 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.29e-01 bond pdb=" CA ARG A 650 " pdb=" CB ARG A 650 " ideal model delta sigma weight residual 1.527 1.541 -0.013 1.61e-02 3.86e+03 6.97e-01 ... (remaining 13453 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.99: 272 105.99 - 113.00: 6882 113.00 - 120.01: 4921 120.01 - 127.03: 5995 127.03 - 134.04: 164 Bond angle restraints: 18234 Sorted by residual: angle pdb=" N GLN B 352 " pdb=" CA GLN B 352 " pdb=" CB GLN B 352 " ideal model delta sigma weight residual 111.84 118.05 -6.21 1.49e+00 4.50e-01 1.74e+01 angle pdb=" C LEU C 592 " pdb=" N MET C 593 " pdb=" CA MET C 593 " ideal model delta sigma weight residual 120.69 132.33 -11.64 2.95e+00 1.15e-01 1.56e+01 angle pdb=" N GLN D 352 " pdb=" CA GLN D 352 " pdb=" CB GLN D 352 " ideal model delta sigma weight residual 111.84 117.53 -5.69 1.49e+00 4.50e-01 1.46e+01 angle pdb=" C TYR B 350 " pdb=" CA TYR B 350 " pdb=" CB TYR B 350 " ideal model delta sigma weight residual 111.50 117.49 -5.99 1.64e+00 3.72e-01 1.34e+01 angle pdb=" C LEU A 592 " pdb=" N MET A 593 " pdb=" CA MET A 593 " ideal model delta sigma weight residual 121.27 132.95 -11.68 3.40e+00 8.65e-02 1.18e+01 ... (remaining 18229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 7370 17.28 - 34.56: 469 34.56 - 51.84: 70 51.84 - 69.11: 6 69.11 - 86.39: 11 Dihedral angle restraints: 7926 sinusoidal: 3158 harmonic: 4768 Sorted by residual: dihedral pdb=" CA PHE A 542 " pdb=" C PHE A 542 " pdb=" N PRO A 543 " pdb=" CA PRO A 543 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE C 542 " pdb=" C PHE C 542 " pdb=" N PRO C 543 " pdb=" CA PRO C 543 " ideal model delta harmonic sigma weight residual 180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP C 505 " pdb=" C TRP C 505 " pdb=" N GLN C 506 " pdb=" CA GLN C 506 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 7923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1353 0.038 - 0.076: 446 0.076 - 0.115: 128 0.115 - 0.153: 21 0.153 - 0.191: 2 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA GLN B 352 " pdb=" N GLN B 352 " pdb=" C GLN B 352 " pdb=" CB GLN B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA GLN D 352 " pdb=" N GLN D 352 " pdb=" C GLN D 352 " pdb=" CB GLN D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA VAL B 262 " pdb=" N VAL B 262 " pdb=" C VAL B 262 " pdb=" CB VAL B 262 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1947 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 567 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 568 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 568 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 568 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 410 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 411 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 567 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 568 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " -0.027 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 432 2.71 - 3.26: 13628 3.26 - 3.81: 22621 3.81 - 4.35: 29042 4.35 - 4.90: 48029 Nonbonded interactions: 113752 Sorted by model distance: nonbonded pdb=" OG SER D 286 " pdb=" OD1 ASP D 316 " model vdw 2.167 2.440 nonbonded pdb=" O LEU D 209 " pdb=" OH TYR D 315 " model vdw 2.178 2.440 nonbonded pdb=" OG SER C 690 " pdb=" OG1 THR C 722 " model vdw 2.179 2.440 nonbonded pdb=" O ILE A 534 " pdb=" OG1 THR A 538 " model vdw 2.180 2.440 nonbonded pdb=" OG SER A 690 " pdb=" OG1 THR A 722 " model vdw 2.205 2.440 ... (remaining 113747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.49 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.860 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.770 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 0.033 13458 Z= 0.185 Angle : 0.550 11.682 18234 Z= 0.287 Chirality : 0.041 0.191 1950 Planarity : 0.004 0.054 2360 Dihedral : 11.591 86.392 4848 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1606 helix: 0.86 (0.20), residues: 774 sheet: -0.41 (0.40), residues: 166 loop : -0.53 (0.25), residues: 666 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.442 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 262 average time/residue: 1.2890 time to fit residues: 367.2297 Evaluate side-chains 224 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.0354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13458 Z= 0.209 Angle : 0.576 9.753 18234 Z= 0.299 Chirality : 0.042 0.155 1950 Planarity : 0.005 0.054 2360 Dihedral : 4.366 18.990 1812 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.51 % 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: 0.15 (0.21), residues: 1606 helix: 0.93 (0.19), residues: 802 sheet: -0.69 (0.39), residues: 166 loop : -0.65 (0.25), residues: 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 248 time to evaluate : 1.491 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 254 average time/residue: 1.2291 time to fit residues: 341.2123 Evaluate side-chains 244 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 234 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 7 average time/residue: 0.4556 time to fit residues: 6.0290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 146 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN A 689 GLN B 201 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13458 Z= 0.199 Angle : 0.562 8.221 18234 Z= 0.289 Chirality : 0.041 0.146 1950 Planarity : 0.004 0.049 2360 Dihedral : 4.332 18.921 1812 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 2.44 % 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: 0.26 (0.21), residues: 1606 helix: 1.06 (0.19), residues: 796 sheet: -0.86 (0.39), residues: 166 loop : -0.57 (0.25), residues: 644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 239 time to evaluate : 1.527 Fit side-chains outliers start: 34 outliers final: 12 residues processed: 255 average time/residue: 1.1957 time to fit residues: 334.3696 Evaluate side-chains 241 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 7 average time/residue: 0.6552 time to fit residues: 7.3382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13458 Z= 0.258 Angle : 0.596 10.639 18234 Z= 0.305 Chirality : 0.043 0.145 1950 Planarity : 0.005 0.050 2360 Dihedral : 4.427 19.556 1812 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1606 helix: 1.19 (0.19), residues: 772 sheet: -0.95 (0.39), residues: 166 loop : -0.60 (0.24), residues: 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 232 time to evaluate : 1.541 Fit side-chains outliers start: 27 outliers final: 11 residues processed: 243 average time/residue: 1.2486 time to fit residues: 331.9738 Evaluate side-chains 243 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 232 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.8470 time to fit residues: 6.8323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 GLN ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 13458 Z= 0.326 Angle : 0.610 9.427 18234 Z= 0.317 Chirality : 0.044 0.145 1950 Planarity : 0.005 0.050 2360 Dihedral : 4.580 19.482 1812 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 2.08 % 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: 0.16 (0.21), residues: 1606 helix: 1.05 (0.19), residues: 784 sheet: -1.09 (0.38), residues: 166 loop : -0.64 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 1.512 Fit side-chains outliers start: 29 outliers final: 15 residues processed: 250 average time/residue: 1.2729 time to fit residues: 348.1030 Evaluate side-chains 244 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 7 average time/residue: 0.6260 time to fit residues: 7.1380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.3980 chunk 141 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.0070 chunk 38 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13458 Z= 0.201 Angle : 0.585 10.057 18234 Z= 0.298 Chirality : 0.041 0.142 1950 Planarity : 0.004 0.047 2360 Dihedral : 4.469 19.468 1812 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 2.37 % 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: 0.14 (0.21), residues: 1606 helix: 1.02 (0.19), residues: 798 sheet: -1.10 (0.39), residues: 166 loop : -0.65 (0.25), residues: 642 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 1.469 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 241 average time/residue: 1.2978 time to fit residues: 341.7402 Evaluate side-chains 245 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 229 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.6435 time to fit residues: 5.8053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.0270 chunk 17 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13458 Z= 0.179 Angle : 0.584 10.078 18234 Z= 0.296 Chirality : 0.041 0.144 1950 Planarity : 0.004 0.047 2360 Dihedral : 4.367 19.139 1812 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1606 helix: 1.13 (0.19), residues: 796 sheet: -1.20 (0.39), residues: 166 loop : -0.65 (0.25), residues: 644 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 1.480 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 240 average time/residue: 1.2504 time to fit residues: 329.3061 Evaluate side-chains 234 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 222 time to evaluate : 1.419 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.8641 time to fit residues: 4.9794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13458 Z= 0.249 Angle : 0.616 10.240 18234 Z= 0.315 Chirality : 0.042 0.145 1950 Planarity : 0.005 0.061 2360 Dihedral : 4.445 18.989 1812 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 1.94 % 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: 0.18 (0.21), residues: 1606 helix: 1.10 (0.19), residues: 798 sheet: -1.19 (0.38), residues: 166 loop : -0.68 (0.25), residues: 642 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.509 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 235 average time/residue: 1.1497 time to fit residues: 297.3117 Evaluate side-chains 239 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.4688 time to fit residues: 6.1956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 63 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13458 Z= 0.222 Angle : 0.612 10.774 18234 Z= 0.311 Chirality : 0.042 0.146 1950 Planarity : 0.005 0.048 2360 Dihedral : 4.432 19.005 1812 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.65 % 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: 0.19 (0.21), residues: 1606 helix: 1.13 (0.19), residues: 796 sheet: -1.23 (0.38), residues: 166 loop : -0.69 (0.25), residues: 644 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 224 time to evaluate : 1.489 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 238 average time/residue: 1.2748 time to fit residues: 333.0412 Evaluate side-chains 240 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 7 average time/residue: 0.5534 time to fit residues: 6.7903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13458 Z= 0.258 Angle : 0.633 10.683 18234 Z= 0.322 Chirality : 0.043 0.150 1950 Planarity : 0.005 0.048 2360 Dihedral : 4.484 18.991 1812 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 1.22 % 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: 0.21 (0.21), residues: 1606 helix: 1.15 (0.19), residues: 786 sheet: -1.23 (0.38), residues: 166 loop : -0.65 (0.24), residues: 654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 1.443 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 237 average time/residue: 1.2357 time to fit residues: 320.4199 Evaluate side-chains 234 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 3 average time/residue: 0.8662 time to fit residues: 4.7588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 132 optimal weight: 0.0030 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095392 restraints weight = 22485.245| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.13 r_work: 0.3354 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13458 Z= 0.235 Angle : 0.632 10.870 18234 Z= 0.321 Chirality : 0.042 0.147 1950 Planarity : 0.005 0.049 2360 Dihedral : 4.475 18.981 1812 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1606 helix: 1.08 (0.19), residues: 798 sheet: -1.25 (0.38), residues: 166 loop : -0.68 (0.24), residues: 642 =============================================================================== Job complete usr+sys time: 5706.12 seconds wall clock time: 101 minutes 53.81 seconds (6113.81 seconds total)