Starting phenix.real_space_refine on Sat Dec 28 20:17:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v5d_31723/12_2024/7v5d_31723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v5d_31723/12_2024/7v5d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v5d_31723/12_2024/7v5d_31723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v5d_31723/12_2024/7v5d_31723.map" model { file = "/net/cci-nas-00/data/ceres_data/7v5d_31723/12_2024/7v5d_31723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v5d_31723/12_2024/7v5d_31723.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} 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: 5.81, per 1000 atoms: 0.66 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.83 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: 2.50 Time building geometry restraints manager: 2.64 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 - 30.18: 5150 30.18 - 60.35: 197 60.35 - 90.53: 21 90.53 - 120.71: 0 120.71 - 150.88: 1 Dihedral angle restraints: 5369 sinusoidal: 2081 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 5366 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: 2.210 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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= 0.667 Angle : 0.937 8.109 12161 Z= 0.508 Chirality : 0.054 0.235 1431 Planarity : 0.006 0.073 1541 Dihedral : 16.059 150.884 3261 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.003 TRP A 322 HIS 0.007 0.001 HIS A 429 PHE 0.027 0.003 PHE B 272 TYR 0.018 0.002 TYR A 509 ARG 0.023 0.001 ARG A 263 *********************** 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 : 1.179 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: 0.7853 (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: 0.2063 time to fit residues: 36.9202 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 : 1.066 ------------------------------------------------------------------------------- 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 96 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 520 ASN A 618 HIS A 625 GLN ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 HIS A 726 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN B 695 HIS B 716 GLN B 720 HIS B 721 GLN B 722 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8979 Z= 0.369 Angle : 0.666 7.766 12161 Z= 0.355 Chirality : 0.043 0.150 1431 Planarity : 0.004 0.054 1541 Dihedral : 8.514 137.090 1288 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.58 % Allowed : 19.28 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1136 helix: 0.33 (0.19), residues: 730 sheet: -4.26 (0.47), residues: 50 loop : -2.70 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 322 HIS 0.005 0.001 HIS A 429 PHE 0.018 0.002 PHE B 272 TYR 0.018 0.001 TYR A 730 ARG 0.005 0.000 ARG A 651 *********************** 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 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 466 MET cc_start: 0.8118 (tpp) cc_final: 0.7166 (tpp) REVERT: A 616 ASN cc_start: 0.8999 (m-40) cc_final: 0.8448 (t0) REVERT: A 721 GLN cc_start: 0.8091 (pp30) cc_final: 0.7829 (pm20) REVERT: B 330 MET cc_start: 0.8409 (mmt) cc_final: 0.8209 (mmp) REVERT: B 375 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8394 (mmt180) REVERT: B 713 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7448 (ptp-110) outliers start: 34 outliers final: 25 residues processed: 129 average time/residue: 0.1852 time to fit residues: 34.7754 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR 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 394 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 177 THR 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 362 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 461 VAL 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 57 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 678 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2023 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= 0.157 Angle : 0.538 8.580 12161 Z= 0.279 Chirality : 0.039 0.156 1431 Planarity : 0.004 0.048 1541 Dihedral : 7.912 132.513 1288 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.85 % Allowed : 22.23 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1136 helix: 1.32 (0.20), residues: 724 sheet: -3.84 (0.51), residues: 50 loop : -2.53 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 322 HIS 0.002 0.001 HIS A 688 PHE 0.016 0.001 PHE B 250 TYR 0.017 0.001 TYR A 730 ARG 0.003 0.000 ARG A 277 *********************** 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 151 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.7640 (ttm) cc_final: 0.7254 (ttp) REVERT: A 448 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 607 MET cc_start: 0.6561 (mmp) cc_final: 0.5995 (mmm) REVERT: A 616 ASN cc_start: 0.8970 (m-40) cc_final: 0.8393 (t0) REVERT: A 721 GLN cc_start: 0.8101 (pp30) cc_final: 0.7860 (pm20) REVERT: B 375 ARG cc_start: 0.8497 (mmm160) cc_final: 0.8228 (mmt180) REVERT: B 713 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7429 (ptp-110) outliers start: 27 outliers final: 14 residues processed: 141 average time/residue: 0.1972 time to fit residues: 39.2180 Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 484 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2334 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= 0.159 Angle : 0.539 8.987 12161 Z= 0.274 Chirality : 0.039 0.154 1431 Planarity : 0.003 0.042 1541 Dihedral : 7.700 131.573 1285 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.00 % Allowed : 22.55 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1136 helix: 1.52 (0.20), residues: 738 sheet: -3.60 (0.48), residues: 68 loop : -2.54 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 322 HIS 0.004 0.001 HIS B 618 PHE 0.015 0.001 PHE B 250 TYR 0.012 0.001 TYR A 730 ARG 0.005 0.000 ARG A 277 *********************** 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 149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.7692 (ttm) cc_final: 0.7380 (ttp) REVERT: A 607 MET cc_start: 0.6506 (mmp) cc_final: 0.6237 (mmm) REVERT: A 616 ASN cc_start: 0.8977 (m-40) cc_final: 0.8455 (t0) REVERT: A 721 GLN cc_start: 0.8131 (pp30) cc_final: 0.7623 (pm20) REVERT: B 198 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7363 (mm-30) REVERT: B 347 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8545 (mttm) REVERT: B 662 LEU cc_start: 0.8257 (tt) cc_final: 0.8050 (mt) REVERT: B 713 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7508 (ptp-110) outliers start: 38 outliers final: 25 residues processed: 138 average time/residue: 0.1769 time to fit residues: 36.3105 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 353 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 191 LEU 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 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 586 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8979 Z= 0.172 Angle : 0.537 10.052 12161 Z= 0.272 Chirality : 0.039 0.154 1431 Planarity : 0.003 0.044 1541 Dihedral : 7.633 130.020 1285 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.79 % Allowed : 23.39 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1136 helix: 1.73 (0.20), residues: 730 sheet: -3.28 (0.52), residues: 68 loop : -2.48 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.003 0.001 HIS A 429 PHE 0.015 0.001 PHE B 250 TYR 0.025 0.001 TYR B 573 ARG 0.004 0.000 ARG A 277 *********************** 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 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.7680 (ttm) cc_final: 0.7388 (ttp) REVERT: A 466 MET cc_start: 0.7694 (tpp) cc_final: 0.6906 (tpp) REVERT: A 607 MET cc_start: 0.6555 (mmp) cc_final: 0.6297 (mmm) REVERT: A 616 ASN cc_start: 0.8955 (m-40) cc_final: 0.8493 (t0) REVERT: A 664 GLU cc_start: 0.7683 (pp20) cc_final: 0.7378 (pp20) REVERT: A 721 GLN cc_start: 0.7865 (pp30) cc_final: 0.7617 (pm20) REVERT: B 198 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7387 (mm-30) REVERT: B 662 LEU cc_start: 0.8240 (tt) cc_final: 0.8038 (mt) REVERT: B 713 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7550 (ptp-110) outliers start: 36 outliers final: 31 residues processed: 133 average time/residue: 0.1621 time to fit residues: 32.4484 Evaluate side-chains 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU 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 A residue 692 ILE Chi-restraints excluded: chain B residue 191 LEU 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 422 SER 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 582 SER Chi-restraints excluded: chain B residue 586 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8979 Z= 0.210 Angle : 0.562 9.595 12161 Z= 0.284 Chirality : 0.040 0.153 1431 Planarity : 0.003 0.036 1541 Dihedral : 7.635 129.821 1285 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.85 % Allowed : 22.34 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1136 helix: 1.67 (0.20), residues: 728 sheet: -3.09 (0.53), residues: 68 loop : -2.18 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 322 HIS 0.003 0.001 HIS A 429 PHE 0.015 0.001 PHE B 250 TYR 0.020 0.001 TYR B 573 ARG 0.003 0.000 ARG A 651 *********************** 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 149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.7641 (ttm) cc_final: 0.7341 (ttp) REVERT: A 607 MET cc_start: 0.6557 (mmp) cc_final: 0.6298 (mmm) REVERT: A 616 ASN cc_start: 0.8935 (m-40) cc_final: 0.8505 (t0) REVERT: B 198 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7376 (mm-30) REVERT: B 466 MET cc_start: 0.8057 (mmm) cc_final: 0.7842 (mmm) REVERT: B 662 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8001 (mt) REVERT: B 713 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7537 (ptp-110) outliers start: 46 outliers final: 39 residues processed: 137 average time/residue: 0.1757 time to fit residues: 36.1966 Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 266 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU 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 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 296 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 421 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 518 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 586 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.0570 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8979 Z= 0.148 Angle : 0.550 9.381 12161 Z= 0.272 Chirality : 0.038 0.153 1431 Planarity : 0.003 0.037 1541 Dihedral : 7.510 128.059 1285 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.48 % Allowed : 24.76 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1136 helix: 1.89 (0.20), residues: 738 sheet: -2.70 (0.57), residues: 68 loop : -2.29 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 322 HIS 0.003 0.001 HIS A 618 PHE 0.016 0.001 PHE B 250 TYR 0.017 0.001 TYR B 573 ARG 0.005 0.000 ARG A 277 *********************** 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 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.908 Fit side-chains REVERT: A 330 MET cc_start: 0.7651 (ttm) cc_final: 0.7304 (ttp) REVERT: A 607 MET cc_start: 0.6557 (mmp) cc_final: 0.6278 (mmm) REVERT: A 616 ASN cc_start: 0.8951 (m-40) cc_final: 0.8536 (t0) REVERT: B 401 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 662 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7915 (mt) REVERT: B 710 ASP cc_start: 0.8656 (t0) cc_final: 0.8454 (t0) REVERT: B 713 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7695 (ptp-110) outliers start: 33 outliers final: 26 residues processed: 132 average time/residue: 0.1716 time to fit residues: 34.0446 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 362 THR 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 246 PHE 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 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 582 SER Chi-restraints excluded: chain B residue 586 VAL 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 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 99 optimal weight: 0.0980 chunk 105 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8979 Z= 0.146 Angle : 0.545 8.813 12161 Z= 0.274 Chirality : 0.038 0.155 1431 Planarity : 0.003 0.034 1541 Dihedral : 7.418 127.715 1285 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.58 % Allowed : 24.66 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1136 helix: 1.95 (0.20), residues: 738 sheet: -2.69 (0.58), residues: 72 loop : -2.21 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 322 HIS 0.002 0.000 HIS B 695 PHE 0.016 0.001 PHE B 250 TYR 0.017 0.001 TYR B 573 ARG 0.005 0.000 ARG A 277 *********************** 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 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.899 Fit side-chains REVERT: A 330 MET cc_start: 0.7830 (ttm) cc_final: 0.7561 (ttp) REVERT: A 518 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6441 (tp) REVERT: A 607 MET cc_start: 0.6522 (mmp) cc_final: 0.6244 (mmm) REVERT: A 616 ASN cc_start: 0.8929 (m-40) cc_final: 0.8577 (t0) REVERT: B 218 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7419 (mmp) REVERT: B 401 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 653 LEU cc_start: 0.8752 (mt) cc_final: 0.8475 (mt) REVERT: B 662 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7968 (mt) REVERT: B 710 ASP cc_start: 0.8604 (t0) cc_final: 0.8375 (t0) REVERT: B 713 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7706 (ptp-110) outliers start: 34 outliers final: 24 residues processed: 132 average time/residue: 0.1688 time to fit residues: 33.1474 Evaluate side-chains 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 218 MET Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 296 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 379 ASN A 571 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8979 Z= 0.386 Angle : 0.698 12.122 12161 Z= 0.358 Chirality : 0.044 0.152 1431 Planarity : 0.004 0.036 1541 Dihedral : 7.783 130.029 1285 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.00 % Allowed : 25.18 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1136 helix: 1.44 (0.20), residues: 728 sheet: -2.49 (0.60), residues: 64 loop : -1.98 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 322 HIS 0.006 0.001 HIS A 429 PHE 0.021 0.002 PHE B 272 TYR 0.022 0.002 TYR B 573 ARG 0.007 0.001 ARG A 651 *********************** 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 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.7616 (ttm) cc_final: 0.7302 (ttp) REVERT: A 607 MET cc_start: 0.6546 (mmp) cc_final: 0.6041 (mmm) REVERT: A 616 ASN cc_start: 0.8984 (m-40) cc_final: 0.8586 (t0) REVERT: B 713 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7561 (ptp-110) outliers start: 38 outliers final: 34 residues processed: 121 average time/residue: 0.1730 time to fit residues: 31.6735 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 266 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 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 246 PHE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 296 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 421 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 586 VAL 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 675 TYR 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 51 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.0370 chunk 104 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2775 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= 0.187 Angle : 0.602 12.839 12161 Z= 0.299 Chirality : 0.039 0.155 1431 Planarity : 0.003 0.038 1541 Dihedral : 7.407 128.352 1285 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.74 % Allowed : 26.77 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1136 helix: 1.81 (0.20), residues: 726 sheet: -2.52 (0.59), residues: 68 loop : -1.95 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 322 HIS 0.002 0.001 HIS A 429 PHE 0.015 0.001 PHE B 250 TYR 0.016 0.001 TYR B 573 ARG 0.005 0.000 ARG A 277 ********************** 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 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.517 Fit side-chains REVERT: A 330 MET cc_start: 0.7587 (ttm) cc_final: 0.7298 (ttp) REVERT: A 607 MET cc_start: 0.6558 (mmp) cc_final: 0.6014 (mmm) REVERT: A 616 ASN cc_start: 0.8958 (m-40) cc_final: 0.8561 (t0) REVERT: B 218 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7199 (mmp) REVERT: B 713 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7549 (ptp-110) outliers start: 26 outliers final: 23 residues processed: 116 average time/residue: 0.1697 time to fit residues: 30.1346 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 362 THR 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 218 MET Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 PHE 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 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 83 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4233 r_free = 0.4233 target = 0.156787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.114185 restraints weight = 13752.062| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.65 r_work: 0.3421 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8979 Z= 0.200 Angle : 0.599 11.521 12161 Z= 0.299 Chirality : 0.039 0.154 1431 Planarity : 0.003 0.035 1541 Dihedral : 7.313 128.427 1285 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.85 % Allowed : 26.55 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1136 helix: 1.83 (0.20), residues: 726 sheet: -2.55 (0.56), residues: 76 loop : -1.94 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 322 HIS 0.003 0.001 HIS A 429 PHE 0.015 0.001 PHE B 250 TYR 0.017 0.001 TYR B 573 ARG 0.005 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.12 seconds wall clock time: 35 minutes 54.93 seconds (2154.93 seconds total)