Starting phenix.real_space_refine on Sun Aug 24 02:29:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6z_61190/08_2025/9j6z_61190.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6z_61190/08_2025/9j6z_61190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j6z_61190/08_2025/9j6z_61190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6z_61190/08_2025/9j6z_61190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j6z_61190/08_2025/9j6z_61190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6z_61190/08_2025/9j6z_61190.map" } resolution = 3.02 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= 0.001 sd= 0.005 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 57 5.16 5 C 10247 2.51 5 N 2783 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16127 Number of models: 1 Model: "" Number of chains: 7 Chain: "5" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 637 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain breaks: 2 Chain: "6" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3185 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 361} Chain breaks: 8 Chain: "7" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2660 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 307} Chain breaks: 9 Chain: "A" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2871 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain breaks: 5 Chain: "c" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1643 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain breaks: 9 Chain: "o" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3823 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 443} Chain breaks: 5 Chain: "p" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1308 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 152} Chain breaks: 10 Time building chain proxies: 3.41, per 1000 atoms: 0.21 Number of scatterers: 16127 At special positions: 0 Unit cell: (109.14, 130.54, 114.49, 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 57 16.00 O 3040 8.00 N 2783 7.00 C 10247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 353 " distance=2.03 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: 1.19 Conformation dependent library (CDL) restraints added in 669.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3710 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 45 sheets defined 12.5% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain '6' and resid 289 through 293 Processing helix chain '6' and resid 295 through 305 removed outlier: 3.667A pdb=" N ASN 6 305 " --> pdb=" O ARG 6 301 " (cutoff:3.500A) Processing helix chain '6' and resid 397 through 401 Processing helix chain '6' and resid 472 through 476 Processing helix chain '6' and resid 494 through 498 Processing helix chain '6' and resid 556 through 558 No H-bonds generated for 'chain '6' and resid 556 through 558' Processing helix chain '6' and resid 565 through 569 Processing helix chain '7' and resid 270 through 274 Processing helix chain '7' and resid 397 through 401 removed outlier: 3.531A pdb=" N PHE 7 401 " --> pdb=" O LEU 7 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.892A pdb=" N SER A 219 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 284 through 298 removed outlier: 4.084A pdb=" N ASN A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 379 removed outlier: 5.641A pdb=" N GLU A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'c' and resid 299 through 305 removed outlier: 3.607A pdb=" N ASN c 305 " --> pdb=" O ARG c 301 " (cutoff:3.500A) Processing helix chain 'c' and resid 432 through 436 removed outlier: 4.137A pdb=" N LEU c 436 " --> pdb=" O LEU c 433 " (cutoff:3.500A) Processing helix chain 'c' and resid 565 through 571 removed outlier: 3.606A pdb=" N ILE c 568 " --> pdb=" O GLU c 565 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR c 570 " --> pdb=" O GLU c 567 " (cutoff:3.500A) Processing helix chain 'o' and resid 270 through 274 Processing helix chain 'o' and resid 289 through 293 Processing helix chain 'o' and resid 295 through 305 removed outlier: 3.833A pdb=" N ASN o 305 " --> pdb=" O ARG o 301 " (cutoff:3.500A) Processing helix chain 'o' and resid 397 through 401 Processing helix chain 'o' and resid 432 through 436 removed outlier: 3.990A pdb=" N LEU o 436 " --> pdb=" O LEU o 433 " (cutoff:3.500A) Processing helix chain 'o' and resid 494 through 498 removed outlier: 3.538A pdb=" N ASN o 498 " --> pdb=" O THR o 495 " (cutoff:3.500A) Processing helix chain 'o' and resid 565 through 569 Processing helix chain 'p' and resid 270 through 274 Processing helix chain 'p' and resid 397 through 401 Processing sheet with id=AA1, first strand: chain '5' and resid 464 through 467 removed outlier: 6.323A pdb=" N SER 5 466 " --> pdb=" O LEU 5 448 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU 5 448 " --> pdb=" O SER 5 466 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE 6 544 " --> pdb=" O TYR 5 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '5' and resid 481 through 482 removed outlier: 5.977A pdb=" N LEU 5 481 " --> pdb=" O VAL 5 608 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET 5 607 " --> pdb=" O PHE 6 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '5' and resid 595 through 598 removed outlier: 3.693A pdb=" N GLY 5 580 " --> pdb=" O VAL 5 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '6' and resid 232 through 236 Processing sheet with id=AA5, first strand: chain '6' and resid 277 through 283 removed outlier: 7.159A pdb=" N THR 6 280 " --> pdb=" O TYR 6 380 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N TYR 6 380 " --> pdb=" O THR 6 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TRP 6 282 " --> pdb=" O TYR 6 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '6' and resid 427 through 429 Processing sheet with id=AA7, first strand: chain '6' and resid 446 through 450 removed outlier: 5.457A pdb=" N LEU 6 448 " --> pdb=" O SER 6 466 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER 6 466 " --> pdb=" O LEU 6 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '6' and resid 485 through 486 Processing sheet with id=AA9, first strand: chain '6' and resid 490 through 492 Processing sheet with id=AB1, first strand: chain '6' and resid 595 through 598 removed outlier: 3.821A pdb=" N GLY 6 580 " --> pdb=" O VAL 6 598 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 607 through 609 removed outlier: 4.029A pdb=" N MET 6 607 " --> pdb=" O PHE 7 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '6' and resid 621 through 623 removed outlier: 6.158A pdb=" N ALA 6 622 " --> pdb=" O LEU 6 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain '7' and resid 245 through 251 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 245 through 251 current: chain '7' and resid 334 through 337 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '7' and resid 259 through 263 Processing sheet with id=AB6, first strand: chain '7' and resid 384 through 385 Processing sheet with id=AB7, first strand: chain '7' and resid 485 through 486 Processing sheet with id=AB8, first strand: chain '7' and resid 490 through 491 Processing sheet with id=AB9, first strand: chain '7' and resid 544 through 546 Processing sheet with id=AC1, first strand: chain '7' and resid 621 through 623 removed outlier: 6.080A pdb=" N ALA 7 622 " --> pdb=" O LEU 7 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 80 through 87 removed outlier: 6.795A pdb=" N LEU A 94 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A 132 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 179 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 134 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN A 131 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 253 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS A 133 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 256 through 257 removed outlier: 6.089A pdb=" N ALA A 263 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 418 through 421 Processing sheet with id=AC5, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.127A pdb=" N GLY A 426 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 446 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR A 428 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 434 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N MET A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 239 through 241 removed outlier: 7.141A pdb=" N GLU c 686 " --> pdb=" O PRO c 311 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU c 688 " --> pdb=" O PHE c 309 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE c 309 " --> pdb=" O GLU c 688 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN c 690 " --> pdb=" O TRP c 307 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE c 309 " --> pdb=" O HIS c 424 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 428 through 429 removed outlier: 6.398A pdb=" N ALA c 428 " --> pdb=" O ARG c 736 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'c' and resid 446 through 450 removed outlier: 5.443A pdb=" N LEU c 448 " --> pdb=" O SER c 466 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER c 466 " --> pdb=" O LEU c 448 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 595 through 598 removed outlier: 3.742A pdb=" N GLY c 580 " --> pdb=" O VAL c 598 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 607 through 609 removed outlier: 3.837A pdb=" N MET c 607 " --> pdb=" O PHE o 631 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 621 through 622 Processing sheet with id=AD3, first strand: chain 'c' and resid 629 through 631 removed outlier: 3.932A pdb=" N MET p 607 " --> pdb=" O PHE c 631 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'o' and resid 232 through 236 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 239 through 250 current: chain 'o' and resid 334 through 337 Processing sheet with id=AD5, first strand: chain 'o' and resid 259 through 263 Processing sheet with id=AD6, first strand: chain 'o' and resid 384 through 385 Processing sheet with id=AD7, first strand: chain 'o' and resid 427 through 429 Processing sheet with id=AD8, first strand: chain 'o' and resid 446 through 447 Processing sheet with id=AD9, first strand: chain 'o' and resid 481 through 482 removed outlier: 6.301A pdb=" N LEU o 481 " --> pdb=" O VAL o 608 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET o 607 " --> pdb=" O PHE p 631 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'o' and resid 485 through 486 Processing sheet with id=AE2, first strand: chain 'o' and resid 490 through 492 Processing sheet with id=AE3, first strand: chain 'o' and resid 544 through 546 Processing sheet with id=AE4, first strand: chain 'o' and resid 596 through 598 removed outlier: 3.661A pdb=" N GLY o 580 " --> pdb=" O VAL o 598 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'o' and resid 621 through 623 removed outlier: 6.042A pdb=" N ALA o 622 " --> pdb=" O LEU o 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'p' and resid 259 through 263 removed outlier: 4.653A pdb=" N PHE p 276 " --> pdb=" O THR p 382 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'p' and resid 384 through 385 removed outlier: 4.027A pdb=" N GLN p 388 " --> pdb=" O ASN p 385 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'p' and resid 485 through 486 Processing sheet with id=AE9, first strand: chain 'p' and resid 621 through 623 removed outlier: 5.989A pdb=" N ALA p 622 " --> pdb=" O LEU p 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 288 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5070 1.34 - 1.45: 3027 1.45 - 1.57: 8384 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 16573 Sorted by residual: bond pdb=" C TYR A 59 " pdb=" N HIS A 60 " ideal model delta sigma weight residual 1.328 1.372 -0.045 1.61e-02 3.86e+03 7.71e+00 bond pdb=" N GLU A 62 " pdb=" CA GLU A 62 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.48e+00 bond pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.07e+00 bond pdb=" N GLU A 61 " pdb=" CA GLU A 61 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.25e-02 6.40e+03 5.90e+00 bond pdb=" N HIS A 60 " pdb=" CA HIS A 60 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.41e-02 5.03e+03 5.85e+00 ... (remaining 16568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 21794 1.31 - 2.63: 572 2.63 - 3.94: 145 3.94 - 5.26: 11 5.26 - 6.57: 1 Bond angle restraints: 22523 Sorted by residual: angle pdb=" CA GLY 7 523 " pdb=" C GLY 7 523 " pdb=" O GLY 7 523 " ideal model delta sigma weight residual 122.74 118.25 4.49 1.30e+00 5.92e-01 1.19e+01 angle pdb=" CA GLU A 61 " pdb=" C GLU A 61 " pdb=" O GLU A 61 " ideal model delta sigma weight residual 121.44 117.72 3.72 1.08e+00 8.57e-01 1.19e+01 angle pdb=" CA ALA 7 520 " pdb=" C ALA 7 520 " pdb=" O ALA 7 520 " ideal model delta sigma weight residual 122.41 118.27 4.14 1.21e+00 6.83e-01 1.17e+01 angle pdb=" N ILE 6 568 " pdb=" CA ILE 6 568 " pdb=" C ILE 6 568 " ideal model delta sigma weight residual 112.29 109.69 2.60 9.40e-01 1.13e+00 7.65e+00 angle pdb=" CA LEU A 64 " pdb=" C LEU A 64 " pdb=" O LEU A 64 " ideal model delta sigma weight residual 121.02 117.93 3.09 1.17e+00 7.31e-01 6.96e+00 ... (remaining 22518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8815 17.88 - 35.76: 689 35.76 - 53.64: 95 53.64 - 71.51: 30 71.51 - 89.39: 22 Dihedral angle restraints: 9651 sinusoidal: 3869 harmonic: 5782 Sorted by residual: dihedral pdb=" CA PRO A 266 " pdb=" C PRO A 266 " pdb=" N PHE A 267 " pdb=" CA PHE A 267 " ideal model delta harmonic sigma weight residual -180.00 -153.55 -26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR A 265 " pdb=" C TYR A 265 " pdb=" N PRO A 266 " pdb=" CA PRO A 266 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA MET A 438 " pdb=" C MET A 438 " pdb=" N PRO A 439 " pdb=" CA PRO A 439 " ideal model delta harmonic sigma weight residual 180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 9648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1538 0.032 - 0.064: 568 0.064 - 0.096: 159 0.096 - 0.128: 80 0.128 - 0.161: 6 Chirality restraints: 2351 Sorted by residual: chirality pdb=" CA GLU A 63 " pdb=" N GLU A 63 " pdb=" C GLU A 63 " pdb=" CB GLU A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA ILE A 402 " pdb=" N ILE A 402 " pdb=" C ILE A 402 " pdb=" CB ILE A 402 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" C PRO A 266 " pdb=" CB PRO A 266 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 2348 not shown) Planarity restraints: 2947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG c 301 " 0.126 9.50e-02 1.11e+02 5.71e-02 2.77e+00 pdb=" NE ARG c 301 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG c 301 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG c 301 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG c 301 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 424 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 425 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO 6 645 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO 6 646 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO 6 646 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO 6 646 " -0.019 5.00e-02 4.00e+02 ... (remaining 2944 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 348 2.67 - 3.23: 15349 3.23 - 3.78: 27457 3.78 - 4.34: 39059 4.34 - 4.90: 62230 Nonbonded interactions: 144443 Sorted by model distance: nonbonded pdb=" OD2 ASP 6 298 " pdb=" OH TYR p 400 " model vdw 2.111 3.040 nonbonded pdb=" OH TYR p 258 " pdb=" OE1 GLU p 399 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR 7 400 " pdb=" OD2 ASP o 298 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR o 253 " pdb=" O ILE o 375 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR 7 416 " pdb=" O HIS 7 644 " model vdw 2.177 3.040 ... (remaining 144438 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=1.00 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.920 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.045 16575 Z= 0.143 Angle : 0.539 6.572 22527 Z= 0.297 Chirality : 0.040 0.161 2351 Planarity : 0.004 0.057 2947 Dihedral : 13.776 89.392 5935 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.48 (0.19), residues: 1907 helix: -0.41 (0.38), residues: 165 sheet: -0.24 (0.25), residues: 353 loop : -0.29 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG c 301 TYR 0.015 0.001 TYR A 356 PHE 0.014 0.001 PHE A 267 TRP 0.018 0.001 TRP o 687 HIS 0.005 0.001 HIS c 424 Details of bonding type rmsd covalent geometry : bond 0.00286 (16573) covalent geometry : angle 0.53838 (22523) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.14524 ( 4) hydrogen bonds : bond 0.18941 ( 288) hydrogen bonds : angle 7.67320 ( 636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 607 MET cc_start: 0.8768 (mtm) cc_final: 0.8414 (mtm) REVERT: 7 333 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8247 (tttt) REVERT: 7 556 ASP cc_start: 0.8690 (t0) cc_final: 0.8197 (t0) REVERT: 7 559 ASP cc_start: 0.8926 (m-30) cc_final: 0.8710 (m-30) REVERT: A 381 HIS cc_start: 0.6167 (m-70) cc_final: 0.5754 (m90) REVERT: c 442 ASP cc_start: 0.8679 (m-30) cc_final: 0.8464 (m-30) REVERT: c 567 GLU cc_start: 0.8658 (mp0) cc_final: 0.8430 (mp0) REVERT: c 700 GLU cc_start: 0.6919 (mp0) cc_final: 0.6683 (pm20) REVERT: p 265 THR cc_start: 0.7595 (p) cc_final: 0.7357 (p) REVERT: p 423 PHE cc_start: 0.8664 (m-80) cc_final: 0.8392 (m-80) REVERT: p 620 ILE cc_start: 0.7101 (mp) cc_final: 0.6895 (mm) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1465 time to fit residues: 62.9253 Evaluate side-chains 155 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 479 ASN ** 5 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 554 ASN A 131 GLN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 611 ASN c 632 HIS o 254 ASN o 344 GLN o 611 ASN ** p 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.069345 restraints weight = 35936.413| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.83 r_work: 0.2844 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16575 Z= 0.215 Angle : 0.572 9.157 22527 Z= 0.296 Chirality : 0.042 0.158 2351 Planarity : 0.004 0.044 2947 Dihedral : 4.930 57.252 2168 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.86 % Allowed : 6.64 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.33 (0.19), residues: 1907 helix: 0.03 (0.40), residues: 170 sheet: -0.12 (0.25), residues: 351 loop : -0.24 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 5 450 TYR 0.017 0.002 TYR p 275 PHE 0.015 0.002 PHE A 267 TRP 0.009 0.001 TRP c 687 HIS 0.008 0.001 HIS 7 291 Details of bonding type rmsd covalent geometry : bond 0.00498 (16573) covalent geometry : angle 0.57128 (22523) SS BOND : bond 0.01808 ( 2) SS BOND : angle 2.29406 ( 4) hydrogen bonds : bond 0.03600 ( 288) hydrogen bonds : angle 5.84354 ( 636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 405 MET cc_start: 0.9079 (mtt) cc_final: 0.8838 (mtp) REVERT: A 61 GLU cc_start: 0.7590 (tt0) cc_final: 0.7383 (tt0) REVERT: A 246 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8182 (ptm160) REVERT: A 335 GLN cc_start: 0.8844 (pt0) cc_final: 0.8403 (pt0) REVERT: A 381 HIS cc_start: 0.6825 (m-70) cc_final: 0.6081 (m90) REVERT: c 442 ASP cc_start: 0.8868 (m-30) cc_final: 0.8592 (m-30) REVERT: c 644 HIS cc_start: 0.8779 (m-70) cc_final: 0.8565 (m90) REVERT: c 700 GLU cc_start: 0.7169 (mp0) cc_final: 0.6789 (pm20) REVERT: o 388 GLN cc_start: 0.7604 (tt0) cc_final: 0.7169 (tp40) REVERT: p 265 THR cc_start: 0.7842 (p) cc_final: 0.7589 (p) REVERT: p 399 GLU cc_start: 0.8964 (mp0) cc_final: 0.8602 (mp0) REVERT: p 620 ILE cc_start: 0.7070 (mp) cc_final: 0.6838 (mm) outliers start: 15 outliers final: 9 residues processed: 165 average time/residue: 0.1430 time to fit residues: 33.5911 Evaluate side-chains 144 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 7 residue 598 VAL Chi-restraints excluded: chain 7 residue 678 THR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain c residue 591 THR Chi-restraints excluded: chain c residue 598 VAL Chi-restraints excluded: chain c residue 600 SER Chi-restraints excluded: chain p residue 526 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 610 GLN ** 6 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 385 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 429 HIS c 587 GLN c 632 HIS o 352 GLN o 554 ASN o 601 GLN ** p 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.066520 restraints weight = 36645.089| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.81 r_work: 0.2787 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16575 Z= 0.281 Angle : 0.572 6.217 22527 Z= 0.294 Chirality : 0.043 0.178 2351 Planarity : 0.004 0.045 2947 Dihedral : 5.008 55.942 2168 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.14 % Allowed : 8.58 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.38 (0.18), residues: 1907 helix: 0.33 (0.42), residues: 170 sheet: -0.18 (0.25), residues: 356 loop : -0.31 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG o 535 TYR 0.016 0.002 TYR p 275 PHE 0.012 0.002 PHE p 631 TRP 0.010 0.001 TRP c 687 HIS 0.011 0.002 HIS 7 291 Details of bonding type rmsd covalent geometry : bond 0.00649 (16573) covalent geometry : angle 0.57121 (22523) SS BOND : bond 0.00731 ( 2) SS BOND : angle 2.02183 ( 4) hydrogen bonds : bond 0.03584 ( 288) hydrogen bonds : angle 5.60047 ( 636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 405 MET cc_start: 0.9146 (mtt) cc_final: 0.8881 (mtp) REVERT: A 131 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: A 223 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7829 (pp30) REVERT: A 246 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8250 (ptm160) REVERT: A 335 GLN cc_start: 0.8866 (pt0) cc_final: 0.8481 (pt0) REVERT: A 381 HIS cc_start: 0.6893 (m-70) cc_final: 0.6208 (m90) REVERT: c 442 ASP cc_start: 0.8952 (m-30) cc_final: 0.8693 (m-30) REVERT: c 700 GLU cc_start: 0.7299 (mp0) cc_final: 0.6688 (pm20) REVERT: o 388 GLN cc_start: 0.8037 (tt0) cc_final: 0.7383 (tp40) REVERT: o 554 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8159 (t0) REVERT: p 265 THR cc_start: 0.8225 (p) cc_final: 0.7982 (p) REVERT: p 399 GLU cc_start: 0.8993 (mp0) cc_final: 0.8579 (mp0) REVERT: p 620 ILE cc_start: 0.7122 (mp) cc_final: 0.6876 (mm) outliers start: 20 outliers final: 13 residues processed: 149 average time/residue: 0.1152 time to fit residues: 25.3614 Evaluate side-chains 146 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 6 residue 236 LEU Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 598 VAL Chi-restraints excluded: chain 7 residue 678 THR Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain c residue 591 THR Chi-restraints excluded: chain c residue 598 VAL Chi-restraints excluded: chain c residue 600 SER Chi-restraints excluded: chain c residue 731 THR Chi-restraints excluded: chain o residue 554 ASN Chi-restraints excluded: chain p residue 637 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 135 optimal weight: 0.9990 chunk 149 optimal weight: 0.0270 chunk 145 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 335 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 587 GLN c 632 HIS o 554 ASN ** p 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.085452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.069299 restraints weight = 36280.964| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.80 r_work: 0.2841 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16575 Z= 0.121 Angle : 0.481 7.034 22527 Z= 0.248 Chirality : 0.039 0.142 2351 Planarity : 0.004 0.045 2947 Dihedral : 4.679 54.319 2168 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.43 % Allowed : 9.55 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.26 (0.19), residues: 1907 helix: 0.53 (0.42), residues: 170 sheet: -0.02 (0.25), residues: 343 loop : -0.28 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 450 TYR 0.012 0.001 TYR p 275 PHE 0.009 0.001 PHE A 267 TRP 0.008 0.001 TRP o 229 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00278 (16573) covalent geometry : angle 0.48031 (22523) SS BOND : bond 0.00433 ( 2) SS BOND : angle 1.47493 ( 4) hydrogen bonds : bond 0.02933 ( 288) hydrogen bonds : angle 5.34752 ( 636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: A 246 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8216 (ptm160) REVERT: A 251 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 335 GLN cc_start: 0.8798 (pt0) cc_final: 0.8300 (pt0) REVERT: A 381 HIS cc_start: 0.6830 (m-70) cc_final: 0.6545 (m-70) REVERT: c 442 ASP cc_start: 0.8865 (m-30) cc_final: 0.8565 (m-30) REVERT: c 450 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7833 (tpp80) REVERT: c 700 GLU cc_start: 0.7227 (mp0) cc_final: 0.6692 (pm20) REVERT: p 265 THR cc_start: 0.8079 (p) cc_final: 0.7869 (p) REVERT: p 399 GLU cc_start: 0.8944 (mp0) cc_final: 0.8489 (mp0) REVERT: p 620 ILE cc_start: 0.7027 (mp) cc_final: 0.6775 (mm) outliers start: 25 outliers final: 15 residues processed: 155 average time/residue: 0.1243 time to fit residues: 28.2006 Evaluate side-chains 145 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 6 residue 236 LEU Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 678 THR Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain c residue 526 MET Chi-restraints excluded: chain c residue 591 THR Chi-restraints excluded: chain c residue 598 VAL Chi-restraints excluded: chain c residue 600 SER Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 240 VAL Chi-restraints excluded: chain p residue 637 MET Chi-restraints excluded: chain p residue 663 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 6 optimal weight: 0.4980 chunk 176 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 110 optimal weight: 40.0000 chunk 147 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 385 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 = 0.3241 r_free = 0.3241 target = 0.085440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069265 restraints weight = 36122.035| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.79 r_work: 0.2839 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16575 Z= 0.132 Angle : 0.474 7.036 22527 Z= 0.243 Chirality : 0.039 0.138 2351 Planarity : 0.004 0.045 2947 Dihedral : 4.549 53.872 2168 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.37 % Allowed : 10.01 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.15 (0.19), residues: 1907 helix: 0.64 (0.42), residues: 172 sheet: 0.16 (0.25), residues: 352 loop : -0.23 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 450 TYR 0.012 0.001 TYR p 275 PHE 0.008 0.001 PHE o 631 TRP 0.007 0.001 TRP A 244 HIS 0.005 0.001 HIS 7 291 Details of bonding type rmsd covalent geometry : bond 0.00307 (16573) covalent geometry : angle 0.47380 (22523) SS BOND : bond 0.00327 ( 2) SS BOND : angle 1.25798 ( 4) hydrogen bonds : bond 0.02847 ( 288) hydrogen bonds : angle 5.13950 ( 636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 7 413 GLN cc_start: 0.8324 (pp30) cc_final: 0.8090 (pp30) REVERT: A 131 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: A 246 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8104 (ptm160) REVERT: A 251 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8449 (p) REVERT: A 326 HIS cc_start: 0.8685 (t70) cc_final: 0.8482 (t-90) REVERT: A 335 GLN cc_start: 0.8813 (pt0) cc_final: 0.8248 (pt0) REVERT: A 381 HIS cc_start: 0.6928 (m-70) cc_final: 0.6651 (m-70) REVERT: c 442 ASP cc_start: 0.8852 (m-30) cc_final: 0.8637 (m-30) REVERT: c 450 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7925 (tpp80) REVERT: c 628 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8878 (t0) REVERT: c 700 GLU cc_start: 0.7243 (mp0) cc_final: 0.6709 (pm20) REVERT: p 399 GLU cc_start: 0.8907 (mp0) cc_final: 0.8403 (mp0) REVERT: p 620 ILE cc_start: 0.7030 (mp) cc_final: 0.6753 (mm) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.1305 time to fit residues: 28.8919 Evaluate side-chains 149 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 5 residue 589 GLN Chi-restraints excluded: chain 6 residue 236 LEU Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 6 residue 681 VAL Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 598 VAL Chi-restraints excluded: chain 7 residue 678 THR Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain c residue 526 MET Chi-restraints excluded: chain c residue 591 THR Chi-restraints excluded: chain c residue 598 VAL Chi-restraints excluded: chain c residue 600 SER Chi-restraints excluded: chain c residue 628 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 240 VAL Chi-restraints excluded: chain p residue 637 MET Chi-restraints excluded: chain p residue 663 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 127 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 343 ASN ** p 385 ASN ** 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 = 0.3234 r_free = 0.3234 target = 0.085120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068790 restraints weight = 35981.324| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.80 r_work: 0.2832 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16575 Z= 0.145 Angle : 0.475 7.473 22527 Z= 0.243 Chirality : 0.040 0.137 2351 Planarity : 0.004 0.045 2947 Dihedral : 4.513 52.632 2168 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.43 % Allowed : 10.47 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.07 (0.19), residues: 1907 helix: 0.77 (0.42), residues: 172 sheet: 0.24 (0.26), residues: 343 loop : -0.20 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 450 TYR 0.013 0.001 TYR p 275 PHE 0.009 0.001 PHE o 631 TRP 0.007 0.001 TRP c 687 HIS 0.006 0.001 HIS 7 291 Details of bonding type rmsd covalent geometry : bond 0.00337 (16573) covalent geometry : angle 0.47431 (22523) SS BOND : bond 0.00300 ( 2) SS BOND : angle 1.19188 ( 4) hydrogen bonds : bond 0.02762 ( 288) hydrogen bonds : angle 5.04716 ( 636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 7 413 GLN cc_start: 0.8362 (pp30) cc_final: 0.8126 (pp30) REVERT: A 131 GLN cc_start: 0.7854 (mt0) cc_final: 0.7436 (pt0) REVERT: A 246 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8096 (ptm160) REVERT: A 251 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8507 (p) REVERT: A 334 MET cc_start: 0.8237 (tmm) cc_final: 0.7924 (tmm) REVERT: A 335 GLN cc_start: 0.8793 (pt0) cc_final: 0.8145 (pt0) REVERT: A 381 HIS cc_start: 0.7070 (m-70) cc_final: 0.6762 (m-70) REVERT: c 450 ARG cc_start: 0.8372 (tpp80) cc_final: 0.8141 (tpp80) REVERT: c 628 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8858 (t0) REVERT: p 399 GLU cc_start: 0.8942 (mp0) cc_final: 0.8387 (mp0) REVERT: p 620 ILE cc_start: 0.7081 (mp) cc_final: 0.6758 (mm) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 0.1212 time to fit residues: 27.1989 Evaluate side-chains 144 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 589 GLN Chi-restraints excluded: chain 6 residue 236 LEU Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 342 THR Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 598 VAL Chi-restraints excluded: chain 7 residue 678 THR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain c residue 526 MET Chi-restraints excluded: chain c residue 532 ASP Chi-restraints excluded: chain c residue 591 THR Chi-restraints excluded: chain c residue 598 VAL Chi-restraints excluded: chain c residue 600 SER Chi-restraints excluded: chain c residue 628 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 240 VAL Chi-restraints excluded: chain p residue 637 MET Chi-restraints excluded: chain p residue 663 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 587 GLN ** p 385 ASN ** 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 = 0.3200 r_free = 0.3200 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.067026 restraints weight = 36298.286| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.77 r_work: 0.2785 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16575 Z= 0.218 Angle : 0.513 6.912 22527 Z= 0.262 Chirality : 0.041 0.148 2351 Planarity : 0.004 0.045 2947 Dihedral : 4.694 55.349 2168 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 10.70 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.09 (0.19), residues: 1907 helix: 0.83 (0.43), residues: 170 sheet: 0.19 (0.26), residues: 343 loop : -0.20 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 490 TYR 0.014 0.002 TYR p 275 PHE 0.016 0.001 PHE A 224 TRP 0.007 0.001 TRP 5 480 HIS 0.009 0.001 HIS 7 291 Details of bonding type rmsd covalent geometry : bond 0.00506 (16573) covalent geometry : angle 0.51280 (22523) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.31965 ( 4) hydrogen bonds : bond 0.02961 ( 288) hydrogen bonds : angle 5.13065 ( 636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: 5 473 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8704 (mtt) REVERT: 5 476 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: 7 566 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5710 (mt-10) REVERT: A 131 GLN cc_start: 0.7863 (mt0) cc_final: 0.6996 (pt0) REVERT: A 251 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 335 GLN cc_start: 0.8809 (pt0) cc_final: 0.8196 (pt0) REVERT: A 381 HIS cc_start: 0.7171 (m-70) cc_final: 0.6861 (m-70) REVERT: c 442 ASP cc_start: 0.8811 (m-30) cc_final: 0.8594 (m-30) REVERT: c 628 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8838 (t0) REVERT: o 399 GLU cc_start: 0.5190 (OUTLIER) cc_final: 0.4606 (pt0) REVERT: p 399 GLU cc_start: 0.8951 (mp0) cc_final: 0.8377 (mp0) REVERT: p 620 ILE cc_start: 0.6993 (mp) cc_final: 0.6659 (mm) outliers start: 30 outliers final: 20 residues processed: 150 average time/residue: 0.1233 time to fit residues: 27.9228 Evaluate side-chains 149 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 5 residue 473 MET Chi-restraints excluded: chain 5 residue 476 GLN Chi-restraints excluded: chain 5 residue 589 GLN Chi-restraints excluded: chain 6 residue 236 LEU Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 342 THR Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 598 VAL Chi-restraints excluded: chain 7 residue 678 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain c residue 526 MET Chi-restraints excluded: chain c residue 532 ASP Chi-restraints excluded: chain c residue 591 THR Chi-restraints excluded: chain c residue 598 VAL Chi-restraints excluded: chain c residue 600 SER Chi-restraints excluded: chain c residue 628 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 240 VAL Chi-restraints excluded: chain o residue 399 GLU Chi-restraints excluded: chain p residue 637 MET Chi-restraints excluded: chain p residue 663 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 55 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 675 GLN c 431 GLN c 587 GLN o 702 GLN ** p 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.065462 restraints weight = 36623.145| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.76 r_work: 0.2752 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 16575 Z= 0.292 Angle : 0.572 6.270 22527 Z= 0.293 Chirality : 0.043 0.156 2351 Planarity : 0.004 0.044 2947 Dihedral : 5.004 61.867 2168 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.95 % Allowed : 10.98 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 aren not related in a simple way. whole: -0.26 (0.19), residues: 1907 helix: 0.72 (0.42), residues: 168 sheet: -0.16 (0.25), residues: 368 loop : -0.25 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 7 490 TYR 0.018 0.002 TYR p 275 PHE 0.014 0.002 PHE c 631 TRP 0.009 0.001 TRP p 282 HIS 0.012 0.002 HIS 7 291 Details of bonding type rmsd covalent geometry : bond 0.00678 (16573) covalent geometry : angle 0.57147 (22523) SS BOND : bond 0.00468 ( 2) SS BOND : angle 1.55653 ( 4) hydrogen bonds : bond 0.03267 ( 288) hydrogen bonds : angle 5.33769 ( 636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.645 Fit side-chains REVERT: 5 473 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8804 (mtt) REVERT: 5 476 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8814 (tt0) REVERT: 7 566 GLU cc_start: 0.6266 (mt-10) cc_final: 0.5735 (mt-10) REVERT: A 131 GLN cc_start: 0.7839 (mt0) cc_final: 0.7349 (pt0) REVERT: A 251 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8555 (p) REVERT: A 335 GLN cc_start: 0.8671 (pt0) cc_final: 0.8370 (pt0) REVERT: A 381 HIS cc_start: 0.7266 (m-70) cc_final: 0.6970 (m-70) REVERT: A 438 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.4502 (ppp) REVERT: c 628 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8820 (t0) REVERT: o 399 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.4947 (pt0) REVERT: o 420 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8618 (t0) REVERT: o 706 ASN cc_start: 0.8407 (t0) cc_final: 0.7807 (p0) REVERT: p 399 GLU cc_start: 0.9004 (mp0) cc_final: 0.8452 (mp0) outliers start: 34 outliers final: 21 residues processed: 151 average time/residue: 0.1304 time to fit residues: 29.5551 Evaluate side-chains 150 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 5 residue 473 MET Chi-restraints excluded: chain 5 residue 476 GLN Chi-restraints excluded: chain 5 residue 589 GLN Chi-restraints excluded: chain 6 residue 236 LEU Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 6 residue 707 TYR Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 342 THR Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 598 VAL Chi-restraints excluded: chain 7 residue 678 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain c residue 526 MET Chi-restraints excluded: chain c residue 532 ASP Chi-restraints excluded: chain c residue 591 THR Chi-restraints excluded: chain c residue 598 VAL Chi-restraints excluded: chain c residue 600 SER Chi-restraints excluded: chain c residue 628 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 240 VAL Chi-restraints excluded: chain o residue 399 GLU Chi-restraints excluded: chain o residue 420 ASP Chi-restraints excluded: chain p residue 637 MET Chi-restraints excluded: chain p residue 663 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6848 > 50: distance: 83 - 102: 11.889 distance: 90 - 94: 28.138 distance: 94 - 95: 19.984 distance: 95 - 96: 37.791 distance: 95 - 98: 24.728 distance: 96 - 97: 16.169 distance: 96 - 102: 28.309 distance: 97 - 118: 50.708 distance: 98 - 99: 61.379 distance: 98 - 100: 42.804 distance: 99 - 101: 60.548 distance: 102 - 103: 18.896 distance: 103 - 104: 35.867 distance: 103 - 106: 20.836 distance: 104 - 105: 42.799 distance: 104 - 111: 33.328 distance: 106 - 107: 51.856 distance: 107 - 108: 38.944 distance: 108 - 109: 68.363 distance: 109 - 110: 57.333 distance: 111 - 112: 27.706 distance: 112 - 113: 5.785 distance: 112 - 115: 33.834 distance: 113 - 114: 46.470 distance: 113 - 118: 56.202 distance: 115 - 116: 19.960 distance: 115 - 117: 32.354 distance: 118 - 119: 52.699 distance: 119 - 120: 56.428 distance: 119 - 122: 5.749 distance: 120 - 121: 34.617 distance: 120 - 125: 39.597 distance: 122 - 123: 69.441 distance: 122 - 124: 55.907 distance: 126 - 127: 51.750 distance: 126 - 129: 64.504 distance: 127 - 128: 26.175 distance: 127 - 133: 21.487 distance: 129 - 130: 33.930 distance: 130 - 131: 46.484 distance: 130 - 132: 56.396 distance: 133 - 134: 33.949 distance: 133 - 139: 26.065 distance: 134 - 135: 53.405 distance: 134 - 137: 32.897 distance: 135 - 136: 34.792 distance: 135 - 140: 20.242 distance: 137 - 138: 41.795 distance: 138 - 139: 49.944 distance: 140 - 141: 35.545 distance: 141 - 142: 25.886 distance: 141 - 144: 22.332 distance: 142 - 143: 39.997 distance: 142 - 147: 45.491 distance: 144 - 145: 52.812 distance: 144 - 146: 34.147 distance: 147 - 148: 13.064 distance: 148 - 149: 46.557 distance: 148 - 151: 17.720 distance: 149 - 150: 48.775 distance: 149 - 152: 26.719 distance: 152 - 153: 40.521 distance: 153 - 154: 37.028 distance: 153 - 156: 16.332 distance: 154 - 155: 47.595 distance: 154 - 159: 56.294 distance: 156 - 157: 44.573 distance: 156 - 158: 56.255 distance: 159 - 160: 9.782 distance: 160 - 161: 29.656 distance: 160 - 163: 64.250 distance: 161 - 162: 45.808 distance: 161 - 168: 34.101 distance: 163 - 164: 42.698 distance: 164 - 165: 46.185 distance: 165 - 166: 32.363 distance: 165 - 167: 41.968