Starting phenix.real_space_refine on Thu Jul 2 14:59:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v5d_31723/07_2026/7v5d_31723.map" } resolution = 3.4 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= 0.003 sd= 0.056 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 P 1 5.49 5 S 40 5.16 5 C 5652 2.51 5 N 1491 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4392 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4379 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 554} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.17 Number of scatterers: 8822 At special positions: 0 Unit cell: (80.51, 108.73, 137.78, 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) S 40 16.00 P 1 15.00 O 1638 8.00 N 1491 7.00 C 5652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 233.3 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 67.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 214 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.939A pdb=" N THR A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 264 Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 279 through 321 removed outlier: 4.510A pdb=" N LEU A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER A 321 " --> pdb=" O MET A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 369 Proline residue: A 333 - end of helix removed outlier: 3.991A pdb=" N THR A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.614A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 433 removed outlier: 4.505A pdb=" N VAL A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 472 removed outlier: 5.014A pdb=" N SER A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 480 removed outlier: 4.531A pdb=" N PHE A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.635A pdb=" N TYR A 598 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.744A pdb=" N MET A 622 " --> pdb=" O HIS A 618 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 623' Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.769A pdb=" N GLY A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 637' Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'A' and resid 698 through 702 removed outlier: 3.617A pdb=" N ARG A 702 " --> pdb=" O THR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.523A pdb=" N LEU A 723 " --> pdb=" O THR A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.502A pdb=" N LEU B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 214 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 229 through 264 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 279 through 298 removed outlier: 4.471A pdb=" N LEU B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 321 removed outlier: 4.147A pdb=" N SER B 321 " --> pdb=" O MET B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 370 Proline residue: B 333 - end of helix removed outlier: 4.314A pdb=" N THR B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.878A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 434 removed outlier: 4.336A pdb=" N VAL B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 472 removed outlier: 3.933A pdb=" N TYR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.835A pdb=" N PHE B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 549 removed outlier: 3.908A pdb=" N VAL B 545 " --> pdb=" O LYS B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 604 through 614 removed outlier: 3.752A pdb=" N VAL B 608 " --> pdb=" O PRO B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 622 removed outlier: 3.731A pdb=" N MET B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.646A pdb=" N ALA B 637 " --> pdb=" O GLY B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 672 through 679 removed outlier: 3.864A pdb=" N LEU B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 700 removed outlier: 4.140A pdb=" N THR B 699 " --> pdb=" O ARG B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 730 through 738 removed outlier: 3.715A pdb=" N GLN B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 738 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 522 through 524 removed outlier: 3.816A pdb=" N ASP A 501 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 560 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 659 through 660 removed outlier: 6.790A pdb=" N LEU A 660 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE A 693 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 692 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 532 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU A 709 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 708 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 713 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 518 through 521 removed outlier: 5.729A pdb=" N GLN B 519 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE B 507 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE B 502 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 560 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN B 504 " --> pdb=" O ARG B 558 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG B 558 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 659 through 663 removed outlier: 3.831A pdb=" N LEU B 660 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 692 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA B 532 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LEU B 709 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 534 " --> pdb=" O LEU B 709 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL B 708 " --> pdb=" O VAL B 715 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2486 1.33 - 1.45: 1498 1.45 - 1.57: 4921 1.57 - 1.69: 2 1.69 - 1.81: 72 Bond restraints: 8979 Sorted by residual: bond pdb=" CA ARG B 284 " pdb=" C ARG B 284 " ideal model delta sigma weight residual 1.522 1.431 0.091 1.72e-02 3.38e+03 2.81e+01 bond pdb=" N LEU A 729 " pdb=" CA LEU A 729 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.58e+00 bond pdb=" O4P PGT A 801 " pdb=" P PGT A 801 " ideal model delta sigma weight residual 1.641 1.581 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" CB ASN A 254 " pdb=" CG ASN A 254 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ASN B 254 " pdb=" CG ASN B 254 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.44e+00 ... (remaining 8974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 11272 1.62 - 3.24: 705 3.24 - 4.87: 144 4.87 - 6.49: 25 6.49 - 8.11: 15 Bond angle restraints: 12161 Sorted by residual: angle pdb=" C GLY A 728 " pdb=" N LEU A 729 " pdb=" CA LEU A 729 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C GLN A 298 " pdb=" N ASN A 299 " pdb=" CA ASN A 299 " ideal model delta sigma weight residual 121.52 114.86 6.66 1.84e+00 2.95e-01 1.31e+01 angle pdb=" C VAL B 228 " pdb=" N CYS B 229 " pdb=" CA CYS B 229 " ideal model delta sigma weight residual 121.54 115.03 6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CA ARG B 284 " pdb=" C ARG B 284 " pdb=" N LEU B 285 " ideal model delta sigma weight residual 118.59 123.64 -5.05 1.63e+00 3.76e-01 9.59e+00 angle pdb=" C PHE B 189 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " ideal model delta sigma weight residual 120.72 115.55 5.17 1.67e+00 3.59e-01 9.57e+00 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4681 17.91 - 35.81: 557 35.81 - 53.71: 88 53.71 - 71.62: 16 71.62 - 89.52: 12 Dihedral angle restraints: 5354 sinusoidal: 2066 harmonic: 3288 Sorted by residual: dihedral pdb=" CA MET B 218 " pdb=" C MET B 218 " pdb=" N ASP B 219 " pdb=" CA ASP B 219 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA MET A 218 " pdb=" C MET A 218 " pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ILE A 596 " pdb=" C ILE A 596 " pdb=" N SER A 597 " pdb=" CA SER A 597 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 5351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 934 0.047 - 0.094: 380 0.094 - 0.141: 93 0.141 - 0.188: 20 0.188 - 0.235: 4 Chirality restraints: 1431 Sorted by residual: chirality pdb=" C5 PGT A 801 " pdb=" C4 PGT A 801 " pdb=" C6 PGT A 801 " pdb=" O5 PGT A 801 " both_signs ideal model delta sigma weight residual False -2.30 -2.53 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2 PGT A 801 " pdb=" C1 PGT A 801 " pdb=" C3 PGT A 801 " pdb=" O2 PGT A 801 " both_signs ideal model delta sigma weight residual False 2.35 2.57 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL B 266 " pdb=" CA VAL B 266 " pdb=" CG1 VAL B 266 " pdb=" CG2 VAL B 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1428 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 296 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C VAL A 296 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL A 296 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 297 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 178 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 179 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 229 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C CYS B 229 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS B 229 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 230 " 0.017 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1613 2.75 - 3.29: 9019 3.29 - 3.83: 14187 3.83 - 4.36: 15651 4.36 - 4.90: 27001 Nonbonded interactions: 67471 Sorted by model distance: nonbonded pdb=" O ARG A 651 " pdb=" NH1 ARG A 655 " model vdw 2.215 3.120 nonbonded pdb=" O SER A 433 " pdb=" OG SER A 433 " model vdw 2.239 3.040 nonbonded pdb=" O PRO B 493 " pdb=" OH TYR B 573 " model vdw 2.251 3.040 nonbonded pdb=" OG SER B 640 " pdb=" OE1 GLN B 643 " model vdw 2.262 3.040 nonbonded pdb=" O ILE B 677 " pdb=" N ILE B 681 " model vdw 2.266 3.120 ... (remaining 67466 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 169 through 669 or (resid 670 through 672 and (name N or n \ ame CA or name C or name O or name CB )) or resid 673 through 677 or (resid 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 3 or (resid 684 and (name N or name CA or name C or name O or name CB )) or resi \ d 685 through 686 or (resid 687 and (name N or name CA or name C or name O or na \ me CB )) or resid 688 through 695 or (resid 696 and (name N or name CA or name C \ or name O or name CB )) or resid 697 through 735 or (resid 736 through 737 and \ (name N or name CA or name C or name O or name CB )) or resid 738)) selection = (chain 'B' and (resid 169 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 634 or (resid 635 and (name N \ or name CA or name C or name O or name CB )) or resid 636 through 665 or (resid \ 666 through 672 and (name N or name CA or name C or name O or name CB )) or resi \ d 673 through 734 or (resid 735 through 737 and (name N or name CA or name C or \ name O or name CB )) or resid 738)) } 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: 1.230 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.040 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.010 0.091 8979 Z= 0.436 Angle : 0.937 8.109 12161 Z= 0.508 Chirality : 0.054 0.235 1431 Planarity : 0.006 0.073 1541 Dihedral : 15.766 89.525 3246 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.63 % Allowed : 13.28 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.23), residues: 1136 helix: -0.95 (0.17), residues: 724 sheet: -4.49 (0.49), residues: 34 loop : -3.20 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 263 TYR 0.018 0.002 TYR A 509 PHE 0.027 0.003 PHE B 272 TRP 0.014 0.003 TRP A 322 HIS 0.007 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.01020 / 0.44 ( 8979) covalent geometry : angle 0.93705 / 0.51 (12161) hydrogen bonds : bond 0.14041 / 9.50 ( 544) hydrogen bonds : angle 6.04092 / 4.44 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.253 Fit side-chains REVERT: A 607 MET cc_start: 0.6627 (mmm) cc_final: 0.6316 (mmm) REVERT: A 616 ASN cc_start: 0.9056 (m-40) cc_final: 0.8619 (t0) REVERT: A 664 GLU cc_start: 0.7539 (pp20) cc_final: 0.7283 (pp20) REVERT: A 721 GLN cc_start: 0.8008 (pp30) cc_final: 0.7740 (pm20) REVERT: B 375 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8375 (mmt180) REVERT: B 456 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 462 TYR cc_start: 0.8218 (t80) cc_final: 0.7852 (t80) REVERT: B 607 MET cc_start: 0.8628 (mpp) cc_final: 0.8390 (mpp) REVERT: B 713 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7310 (ptp-110) outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.0732 time to fit residues: 13.2967 Evaluate side-chains 94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.0270 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN A 504 ASN A 520 ASN A 618 HIS A 625 GLN A 678 GLN A 688 HIS A 726 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 679 GLN B 695 HIS B 716 GLN B 720 HIS B 722 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108143 restraints weight = 14002.917| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.94 r_work: 0.3265 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8979 Z= 0.132 Angle : 0.547 8.249 12161 Z= 0.287 Chirality : 0.039 0.158 1431 Planarity : 0.004 0.051 1541 Dihedral : 6.527 57.384 1273 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.79 % Allowed : 17.60 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.26), residues: 1136 helix: 0.88 (0.20), residues: 722 sheet: -4.02 (0.50), residues: 50 loop : -2.65 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.019 0.001 TYR A 730 PHE 0.014 0.001 PHE A 272 TRP 0.022 0.002 TRP A 322 HIS 0.003 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 ( 8979) covalent geometry : angle 0.54712 / 0.29 (12161) hydrogen bonds : bond 0.06254 / 4.08 ( 544) hydrogen bonds : angle 4.52962 / 3.41 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.7981 (tpp) cc_final: 0.7306 (tpp) REVERT: A 500 VAL cc_start: 0.7259 (t) cc_final: 0.6964 (m) REVERT: A 616 ASN cc_start: 0.8973 (m-40) cc_final: 0.8365 (t0) REVERT: A 721 GLN cc_start: 0.8030 (pp30) cc_final: 0.7820 (pm20) REVERT: B 381 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8459 (mp0) REVERT: B 607 MET cc_start: 0.8684 (mpp) cc_final: 0.8381 (mpp) REVERT: B 710 ASP cc_start: 0.8807 (t0) cc_final: 0.8430 (t0) outliers start: 17 outliers final: 7 residues processed: 140 average time/residue: 0.0692 time to fit residues: 14.0555 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 707 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 96 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.156717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115192 restraints weight = 13974.294| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.30 r_work: 0.3461 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8979 Z= 0.136 Angle : 0.553 7.784 12161 Z= 0.284 Chirality : 0.039 0.156 1431 Planarity : 0.003 0.044 1541 Dihedral : 6.225 59.353 1270 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.16 % Allowed : 20.02 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1136 helix: 1.43 (0.20), residues: 712 sheet: -3.77 (0.44), residues: 68 loop : -2.48 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 713 TYR 0.016 0.001 TYR A 730 PHE 0.014 0.001 PHE A 272 TRP 0.017 0.002 TRP A 322 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 8979) covalent geometry : angle 0.55319 / 0.28 (12161) hydrogen bonds : bond 0.06122 / 3.99 ( 544) hydrogen bonds : angle 4.43468 / 3.32 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.7690 (ttm) cc_final: 0.7333 (ttp) REVERT: A 366 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: A 466 MET cc_start: 0.8162 (tpp) cc_final: 0.7410 (tpp) REVERT: A 500 VAL cc_start: 0.7494 (t) cc_final: 0.7157 (m) REVERT: A 607 MET cc_start: 0.6608 (mmp) cc_final: 0.6069 (mmm) REVERT: A 616 ASN cc_start: 0.9003 (m-40) cc_final: 0.8427 (t0) REVERT: A 721 GLN cc_start: 0.8089 (pp30) cc_final: 0.7852 (pm20) REVERT: B 466 MET cc_start: 0.8504 (mmm) cc_final: 0.8269 (mtt) REVERT: B 496 LEU cc_start: 0.5517 (OUTLIER) cc_final: 0.5293 (mm) REVERT: B 713 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7537 (ptp-110) outliers start: 30 outliers final: 22 residues processed: 126 average time/residue: 0.0740 time to fit residues: 13.5034 Evaluate side-chains 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 36 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.158677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.117775 restraints weight = 13848.160| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.12 r_work: 0.3498 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8979 Z= 0.118 Angle : 0.525 8.025 12161 Z= 0.267 Chirality : 0.039 0.156 1431 Planarity : 0.003 0.037 1541 Dihedral : 5.926 58.955 1270 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.37 % Allowed : 21.29 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.27), residues: 1136 helix: 1.76 (0.20), residues: 722 sheet: -3.41 (0.50), residues: 68 loop : -2.52 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 499 TYR 0.014 0.001 TYR A 730 PHE 0.014 0.001 PHE B 250 TRP 0.015 0.001 TRP A 322 HIS 0.002 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 8979) covalent geometry : angle 0.52494 / 0.27 (12161) hydrogen bonds : bond 0.05451 / 3.56 ( 544) hydrogen bonds : angle 4.21394 / 3.18 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.7798 (ttm) cc_final: 0.7501 (ttp) REVERT: A 366 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: A 500 VAL cc_start: 0.7568 (t) cc_final: 0.7300 (m) REVERT: A 518 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6611 (tp) REVERT: A 607 MET cc_start: 0.6589 (mmp) cc_final: 0.6066 (mmm) REVERT: A 616 ASN cc_start: 0.8986 (m-40) cc_final: 0.8446 (t0) REVERT: A 721 GLN cc_start: 0.8164 (pp30) cc_final: 0.7696 (pm20) REVERT: B 198 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7904 (mm-30) REVERT: B 496 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.4757 (mm) REVERT: B 573 TYR cc_start: 0.8222 (t80) cc_final: 0.7804 (t80) REVERT: B 710 ASP cc_start: 0.8723 (t0) cc_final: 0.8509 (t0) REVERT: B 713 ARG cc_start: 0.8276 (mtt90) cc_final: 0.7524 (ptp-110) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.0616 time to fit residues: 12.2499 Evaluate side-chains 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.154489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.112619 restraints weight = 13799.045| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.35 r_work: 0.3417 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8979 Z= 0.163 Angle : 0.561 7.178 12161 Z= 0.288 Chirality : 0.041 0.152 1431 Planarity : 0.003 0.040 1541 Dihedral : 5.962 58.368 1270 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.32 % Allowed : 21.07 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1136 helix: 1.66 (0.20), residues: 720 sheet: -3.35 (0.50), residues: 68 loop : -2.31 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.010 0.001 TYR B 204 PHE 0.014 0.001 PHE A 272 TRP 0.013 0.002 TRP A 322 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8979) covalent geometry : angle 0.56117 / 0.29 (12161) hydrogen bonds : bond 0.06200 / 4.04 ( 544) hydrogen bonds : angle 4.35691 / 3.26 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.7716 (ttm) cc_final: 0.7450 (ttp) REVERT: A 466 MET cc_start: 0.7999 (tpp) cc_final: 0.7288 (tpp) REVERT: A 607 MET cc_start: 0.6626 (mmp) cc_final: 0.6093 (mmm) REVERT: A 616 ASN cc_start: 0.9024 (m-40) cc_final: 0.8438 (t0) REVERT: A 721 GLN cc_start: 0.7862 (pp30) cc_final: 0.7622 (pm20) REVERT: B 198 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8019 (mm-30) REVERT: B 466 MET cc_start: 0.8394 (mtt) cc_final: 0.8155 (mmm) REVERT: B 496 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.4793 (mm) REVERT: B 573 TYR cc_start: 0.8265 (t80) cc_final: 0.7840 (t80) REVERT: B 713 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7659 (ptp-110) outliers start: 41 outliers final: 36 residues processed: 131 average time/residue: 0.0636 time to fit residues: 12.7248 Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 695 HIS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 108 optimal weight: 0.0010 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** 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 = 0.4255 r_free = 0.4255 target = 0.160149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.117957 restraints weight = 13727.963| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.19 r_work: 0.3503 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8979 Z= 0.115 Angle : 0.516 6.762 12161 Z= 0.262 Chirality : 0.039 0.154 1431 Planarity : 0.003 0.047 1541 Dihedral : 5.736 59.441 1270 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.69 % Allowed : 22.76 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.27), residues: 1136 helix: 1.83 (0.20), residues: 736 sheet: -2.75 (0.65), residues: 50 loop : -2.35 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.011 0.001 TYR A 730 PHE 0.015 0.001 PHE B 250 TRP 0.013 0.001 TRP A 322 HIS 0.002 0.000 HIS B 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 ( 8979) covalent geometry : angle 0.51589 / 0.26 (12161) hydrogen bonds : bond 0.05314 / 3.47 ( 544) hydrogen bonds : angle 4.14642 / 3.14 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.203 Fit side-chains REVERT: A 330 MET cc_start: 0.7731 (ttm) cc_final: 0.7381 (ttp) REVERT: A 518 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6652 (tp) REVERT: A 607 MET cc_start: 0.6617 (mmp) cc_final: 0.6067 (mmm) REVERT: A 616 ASN cc_start: 0.8987 (m-40) cc_final: 0.8505 (t0) REVERT: B 198 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7919 (mm-30) REVERT: B 466 MET cc_start: 0.8349 (mtt) cc_final: 0.8114 (mmm) REVERT: B 496 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.4835 (mm) REVERT: B 573 TYR cc_start: 0.8093 (t80) cc_final: 0.7779 (t80) REVERT: B 710 ASP cc_start: 0.8724 (t0) cc_final: 0.8505 (t0) REVERT: B 713 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7882 (ptp-110) outliers start: 35 outliers final: 25 residues processed: 134 average time/residue: 0.0602 time to fit residues: 12.1498 Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** 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 = 0.4237 r_free = 0.4237 target = 0.157308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.115884 restraints weight = 13957.865| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.27 r_work: 0.3452 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8979 Z= 0.140 Angle : 0.552 7.712 12161 Z= 0.280 Chirality : 0.040 0.151 1431 Planarity : 0.003 0.038 1541 Dihedral : 5.717 58.947 1270 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.11 % Allowed : 23.50 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 1136 helix: 1.74 (0.20), residues: 740 sheet: -3.02 (0.54), residues: 68 loop : -2.29 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.011 0.001 TYR A 730 PHE 0.015 0.001 PHE B 250 TRP 0.012 0.001 TRP A 322 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8979) covalent geometry : angle 0.55195 / 0.28 (12161) hydrogen bonds : bond 0.05768 / 3.76 ( 544) hydrogen bonds : angle 4.23106 / 3.19 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.275 Fit side-chains REVERT: A 330 MET cc_start: 0.7765 (ttm) cc_final: 0.7411 (ttp) REVERT: A 466 MET cc_start: 0.7883 (tpp) cc_final: 0.7122 (tpp) REVERT: A 607 MET cc_start: 0.6635 (mmp) cc_final: 0.6093 (mmm) REVERT: A 616 ASN cc_start: 0.8967 (m-40) cc_final: 0.8537 (t0) REVERT: B 198 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7941 (mm-30) REVERT: B 347 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8603 (mttm) REVERT: B 573 TYR cc_start: 0.8141 (t80) cc_final: 0.7813 (t80) REVERT: B 662 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7847 (mt) REVERT: B 710 ASP cc_start: 0.8747 (t0) cc_final: 0.8544 (t0) REVERT: B 713 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7886 (ptp-110) outliers start: 39 outliers final: 29 residues processed: 125 average time/residue: 0.0597 time to fit residues: 11.3004 Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN ** B 220 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 = 0.4215 r_free = 0.4215 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.112859 restraints weight = 13863.059| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.42 r_work: 0.3412 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8979 Z= 0.168 Angle : 0.598 10.768 12161 Z= 0.302 Chirality : 0.041 0.153 1431 Planarity : 0.003 0.036 1541 Dihedral : 5.796 59.231 1270 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.53 % Allowed : 22.87 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1136 helix: 1.68 (0.20), residues: 734 sheet: -2.92 (0.55), residues: 68 loop : -2.23 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.012 0.001 TYR A 730 PHE 0.014 0.001 PHE B 250 TRP 0.011 0.001 TRP A 322 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 8979) covalent geometry : angle 0.59784 / 0.30 (12161) hydrogen bonds : bond 0.06294 / 4.09 ( 544) hydrogen bonds : angle 4.36126 / 3.27 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.249 Fit side-chains REVERT: A 330 MET cc_start: 0.7585 (ttm) cc_final: 0.7348 (ttp) REVERT: A 466 MET cc_start: 0.7975 (tpp) cc_final: 0.7218 (tpp) REVERT: A 607 MET cc_start: 0.6644 (mmp) cc_final: 0.6385 (mmm) REVERT: A 616 ASN cc_start: 0.8988 (m-40) cc_final: 0.8537 (t0) REVERT: B 198 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7912 (mm-30) REVERT: B 347 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8589 (mttm) REVERT: B 466 MET cc_start: 0.8562 (mmm) cc_final: 0.8213 (mtt) REVERT: B 662 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7787 (mt) REVERT: B 713 ARG cc_start: 0.8330 (mtt90) cc_final: 0.7890 (ptp-110) outliers start: 43 outliers final: 38 residues processed: 129 average time/residue: 0.0582 time to fit residues: 11.3613 Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 chunk 109 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN ** B 220 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 = 0.4201 r_free = 0.4201 target = 0.153475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109961 restraints weight = 13984.227| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.21 r_work: 0.3402 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8979 Z= 0.200 Angle : 0.638 9.888 12161 Z= 0.327 Chirality : 0.042 0.161 1431 Planarity : 0.003 0.036 1541 Dihedral : 5.943 59.304 1270 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.95 % Allowed : 22.66 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1136 helix: 1.56 (0.20), residues: 732 sheet: -2.87 (0.57), residues: 68 loop : -2.22 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.022 0.001 TYR B 573 PHE 0.015 0.002 PHE B 272 TRP 0.011 0.002 TRP A 322 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 8979) covalent geometry : angle 0.63778 / 0.33 (12161) hydrogen bonds : bond 0.06781 / 4.41 ( 544) hydrogen bonds : angle 4.57324 / 3.40 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 0.191 Fit side-chains REVERT: A 330 MET cc_start: 0.7632 (ttm) cc_final: 0.7372 (ttp) REVERT: A 466 MET cc_start: 0.8011 (tpp) cc_final: 0.7239 (tpp) REVERT: A 607 MET cc_start: 0.6630 (mmp) cc_final: 0.6374 (mmm) REVERT: A 616 ASN cc_start: 0.8983 (m-40) cc_final: 0.8534 (t0) REVERT: B 198 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7913 (mm-30) REVERT: B 662 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7858 (mt) REVERT: B 713 ARG cc_start: 0.8291 (mtt90) cc_final: 0.7655 (ptp-110) outliers start: 47 outliers final: 40 residues processed: 127 average time/residue: 0.0533 time to fit residues: 10.5185 Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** 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 = 0.4234 r_free = 0.4234 target = 0.156777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113881 restraints weight = 13813.507| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.20 r_work: 0.3463 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8979 Z= 0.138 Angle : 0.594 11.341 12161 Z= 0.298 Chirality : 0.039 0.155 1431 Planarity : 0.003 0.038 1541 Dihedral : 5.777 59.448 1270 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.79 % Allowed : 24.24 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.27), residues: 1136 helix: 1.76 (0.20), residues: 734 sheet: -2.66 (0.59), residues: 68 loop : -2.13 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.023 0.001 TYR B 573 PHE 0.015 0.001 PHE B 250 TRP 0.012 0.001 TRP A 322 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 8979) covalent geometry : angle 0.59372 / 0.30 (12161) hydrogen bonds : bond 0.05879 / 3.83 ( 544) hydrogen bonds : angle 4.35754 / 3.28 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.335 Fit side-chains REVERT: A 330 MET cc_start: 0.7661 (ttm) cc_final: 0.7295 (ttp) REVERT: A 607 MET cc_start: 0.6654 (mmp) cc_final: 0.6391 (mmm) REVERT: A 616 ASN cc_start: 0.8944 (m-40) cc_final: 0.8518 (t0) REVERT: B 198 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7874 (mm-30) REVERT: B 218 MET cc_start: 0.7274 (mmp) cc_final: 0.7009 (mmp) REVERT: B 518 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8175 (tp) REVERT: B 662 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7719 (mt) REVERT: B 713 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7675 (ptp-110) outliers start: 36 outliers final: 33 residues processed: 122 average time/residue: 0.0493 time to fit residues: 9.4144 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 GLN ** 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 = 0.4223 r_free = 0.4223 target = 0.155779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.113481 restraints weight = 13782.838| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.39 r_work: 0.3405 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8979 Z= 0.153 Angle : 0.602 11.174 12161 Z= 0.304 Chirality : 0.040 0.155 1431 Planarity : 0.003 0.035 1541 Dihedral : 5.790 59.731 1270 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.11 % Allowed : 23.50 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1136 helix: 1.73 (0.20), residues: 734 sheet: -2.45 (0.58), residues: 72 loop : -2.19 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.026 0.001 TYR B 573 PHE 0.015 0.001 PHE B 250 TRP 0.012 0.001 TRP A 322 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8979) covalent geometry : angle 0.60245 / 0.30 (12161) hydrogen bonds : bond 0.06124 / 3.99 ( 544) hydrogen bonds : angle 4.40186 / 3.30 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.32 seconds wall clock time: 29 minutes 57.93 seconds (1797.93 seconds total)