Starting phenix.real_space_refine on Mon Mar 11 00:51:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/03_2024/7d10_30542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/03_2024/7d10_30542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/03_2024/7d10_30542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/03_2024/7d10_30542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/03_2024/7d10_30542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/03_2024/7d10_30542_updated.pdb" } resolution = 3.52 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4294 2.51 5 N 1000 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 307": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6424 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3176 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3176 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.07, per 1000 atoms: 0.63 Number of scatterers: 6424 At special positions: 0 Unit cell: (101.463, 79.643, 88.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1102 8.00 N 1000 7.00 C 4294 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 0 sheets defined 60.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.789A pdb=" N ASN A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 320 through 341 removed outlier: 3.738A pdb=" N THR A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 357 No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 362 through 388 removed outlier: 3.909A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.648A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 437 through 452 removed outlier: 3.948A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 487 through 497 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.627A pdb=" N ILE A 518 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 525 through 541 removed outlier: 3.606A pdb=" N LEU A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.783A pdb=" N ILE A 607 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.820A pdb=" N LYS A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 628 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.633A pdb=" N ILE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 698 Proline residue: A 676 - end of helix removed outlier: 4.348A pdb=" N PHE A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.741A pdb=" N CYS A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 750 removed outlier: 3.735A pdb=" N LEU A 737 " --> pdb=" O TRP A 733 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.789A pdb=" N ASN B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 320 through 341 removed outlier: 3.738A pdb=" N THR B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 357 No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 362 through 388 removed outlier: 3.908A pdb=" N ALA B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.647A pdb=" N ILE B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 437 through 452 removed outlier: 3.948A pdb=" N ILE B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 487 through 497 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 514 through 522 removed outlier: 3.627A pdb=" N ILE B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 519 - end of helix Processing helix chain 'B' and resid 525 through 541 removed outlier: 3.607A pdb=" N LEU B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 608 removed outlier: 3.783A pdb=" N ILE B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.821A pdb=" N LYS B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 652 through 666 removed outlier: 3.634A pdb=" N ILE B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 698 Proline residue: B 676 - end of helix removed outlier: 4.349A pdb=" N PHE B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 729 removed outlier: 3.741A pdb=" N CYS B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 727 " --> pdb=" O CYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 750 removed outlier: 3.735A pdb=" N LEU B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 746 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 744 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: 1.64 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1592 1.33 - 1.45: 1190 1.45 - 1.57: 3718 1.57 - 1.68: 2 1.68 - 1.80: 46 Bond restraints: 6548 Sorted by residual: bond pdb=" C ALA A 622 " pdb=" N PRO A 623 " ideal model delta sigma weight residual 1.337 1.373 -0.036 1.24e-02 6.50e+03 8.22e+00 bond pdb=" C ALA B 622 " pdb=" N PRO B 623 " ideal model delta sigma weight residual 1.337 1.373 -0.036 1.24e-02 6.50e+03 8.22e+00 bond pdb=" C PHE A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.337 1.359 -0.023 9.80e-03 1.04e+04 5.32e+00 bond pdb=" C PHE B 495 " pdb=" N PRO B 496 " ideal model delta sigma weight residual 1.337 1.359 -0.022 9.80e-03 1.04e+04 5.18e+00 bond pdb=" C ILE B 518 " pdb=" O ILE B 518 " ideal model delta sigma weight residual 1.240 1.216 0.024 1.22e-02 6.72e+03 3.88e+00 ... (remaining 6543 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.87: 104 105.87 - 112.93: 3443 112.93 - 119.99: 2632 119.99 - 127.05: 2688 127.05 - 134.12: 59 Bond angle restraints: 8926 Sorted by residual: angle pdb=" N PRO B 581 " pdb=" CA PRO B 581 " pdb=" CB PRO B 581 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.45e+01 angle pdb=" N PRO A 581 " pdb=" CA PRO A 581 " pdb=" CB PRO A 581 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.44e+01 angle pdb=" N ALA B 517 " pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 111.36 119.01 -7.65 1.09e+00 8.42e-01 4.93e+01 angle pdb=" N ALA A 517 " pdb=" CA ALA A 517 " pdb=" C ALA A 517 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N PRO A 754 " pdb=" CA PRO A 754 " pdb=" CB PRO A 754 " ideal model delta sigma weight residual 103.00 110.65 -7.65 1.10e+00 8.26e-01 4.84e+01 ... (remaining 8921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 3363 11.91 - 23.82: 278 23.82 - 35.73: 79 35.73 - 47.64: 25 47.64 - 59.55: 5 Dihedral angle restraints: 3750 sinusoidal: 1208 harmonic: 2542 Sorted by residual: dihedral pdb=" CA ALA B 707 " pdb=" C ALA B 707 " pdb=" N PHE B 708 " pdb=" CA PHE B 708 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ALA A 707 " pdb=" C ALA A 707 " pdb=" N PHE A 708 " pdb=" CA PHE A 708 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS A 398 " pdb=" C HIS A 398 " pdb=" N SER A 399 " pdb=" CA SER A 399 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 3747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 777 0.058 - 0.116: 275 0.116 - 0.174: 52 0.174 - 0.232: 10 0.232 - 0.289: 4 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA LYS B 520 " pdb=" N LYS B 520 " pdb=" C LYS B 520 " pdb=" CB LYS B 520 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LYS A 520 " pdb=" N LYS A 520 " pdb=" C LYS A 520 " pdb=" CB LYS A 520 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ALA B 517 " pdb=" N ALA B 517 " pdb=" C ALA B 517 " pdb=" CB ALA B 517 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1115 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 518 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO B 519 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO B 519 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 519 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 518 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 519 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 519 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 519 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 515 " 0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLN B 515 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN B 515 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 516 " 0.024 2.00e-02 2.50e+03 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1606 2.78 - 3.31: 5842 3.31 - 3.84: 10101 3.84 - 4.37: 11984 4.37 - 4.90: 20201 Nonbonded interactions: 49734 Sorted by model distance: nonbonded pdb=" O LEU B 438 " pdb=" OG SER B 609 " model vdw 2.249 2.440 nonbonded pdb=" O LEU A 438 " pdb=" OG SER A 609 " model vdw 2.249 2.440 nonbonded pdb=" O SER A 339 " pdb=" OG1 THR A 343 " model vdw 2.295 2.440 nonbonded pdb=" O SER B 339 " pdb=" OG1 THR B 343 " model vdw 2.295 2.440 nonbonded pdb=" O THR A 499 " pdb=" OH TYR A 686 " model vdw 2.341 2.440 ... (remaining 49729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 1.980 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.180 Find NCS groups from input model: 0.350 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.007 0.063 6548 Z= 0.438 Angle : 1.055 10.800 8926 Z= 0.592 Chirality : 0.063 0.289 1118 Planarity : 0.009 0.116 1084 Dihedral : 10.873 59.548 2114 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.94 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % 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: -6.70 (0.15), residues: 872 helix: -4.28 (0.10), residues: 594 sheet: None (None), residues: 0 loop : -4.33 (0.25), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 714 HIS 0.005 0.004 HIS A 695 PHE 0.024 0.003 PHE B 494 TYR 0.025 0.002 TYR B 383 ARG 0.007 0.001 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.666 Fit side-chains REVERT: A 382 MET cc_start: 0.8932 (ttp) cc_final: 0.8508 (ttt) REVERT: A 415 ILE cc_start: 0.9100 (pp) cc_final: 0.8565 (mm) REVERT: A 601 PRO cc_start: 0.6176 (Cg_endo) cc_final: 0.5972 (Cg_exo) REVERT: B 382 MET cc_start: 0.8931 (ttp) cc_final: 0.8565 (ttt) REVERT: B 415 ILE cc_start: 0.9108 (pp) cc_final: 0.8558 (mm) REVERT: B 469 LYS cc_start: 0.6858 (mmpt) cc_final: 0.6636 (mmtt) REVERT: B 601 PRO cc_start: 0.6195 (Cg_endo) cc_final: 0.5992 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1878 time to fit residues: 37.7655 Evaluate side-chains 95 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 474 ASN A 476 ASN A 506 ASN B 298 ASN B 474 ASN B 476 ASN B 506 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6548 Z= 0.171 Angle : 0.555 6.057 8926 Z= 0.290 Chirality : 0.041 0.116 1118 Planarity : 0.005 0.066 1084 Dihedral : 7.599 57.868 974 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.38 % Allowed : 12.96 % Favored : 82.66 % 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: -4.95 (0.21), residues: 872 helix: -2.81 (0.16), residues: 598 sheet: None (None), residues: 0 loop : -4.02 (0.27), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.025 0.002 PHE B 590 TYR 0.009 0.001 TYR B 383 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 415 ILE cc_start: 0.8888 (pp) cc_final: 0.8667 (mm) REVERT: A 485 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 415 ILE cc_start: 0.8888 (pp) cc_final: 0.8662 (mm) REVERT: B 463 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8500 (mttt) REVERT: B 485 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7496 (mm-30) outliers start: 26 outliers final: 12 residues processed: 140 average time/residue: 0.1614 time to fit residues: 31.3063 Evaluate side-chains 124 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 515 GLN B 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6548 Z= 0.206 Angle : 0.541 5.866 8926 Z= 0.283 Chirality : 0.042 0.126 1118 Planarity : 0.004 0.047 1084 Dihedral : 7.132 57.426 974 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.70 % Allowed : 16.33 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.04 (0.24), residues: 872 helix: -2.05 (0.19), residues: 600 sheet: None (None), residues: 0 loop : -3.87 (0.28), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 714 HIS 0.001 0.001 HIS A 695 PHE 0.026 0.002 PHE B 590 TYR 0.006 0.001 TYR B 383 ARG 0.002 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.105 Fit side-chains REVERT: A 415 ILE cc_start: 0.8915 (pp) cc_final: 0.8526 (mm) REVERT: A 463 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8611 (mttt) REVERT: A 485 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 415 ILE cc_start: 0.8932 (pp) cc_final: 0.8547 (mm) REVERT: B 463 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8531 (mttt) REVERT: B 485 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7568 (mm-30) outliers start: 22 outliers final: 19 residues processed: 128 average time/residue: 0.1944 time to fit residues: 33.4753 Evaluate side-chains 129 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6548 Z= 0.180 Angle : 0.519 5.699 8926 Z= 0.269 Chirality : 0.041 0.121 1118 Planarity : 0.004 0.038 1084 Dihedral : 6.801 59.992 974 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.71 % Allowed : 15.82 % Favored : 79.46 % 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: -3.41 (0.26), residues: 872 helix: -1.57 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -3.67 (0.29), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.021 0.001 PHE A 590 TYR 0.005 0.001 TYR A 383 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.717 Fit side-chains REVERT: A 415 ILE cc_start: 0.8941 (pp) cc_final: 0.8646 (mm) REVERT: A 463 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8604 (mttt) REVERT: A 485 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7532 (mm-30) REVERT: B 415 ILE cc_start: 0.8946 (pp) cc_final: 0.8647 (mm) REVERT: B 463 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8537 (mttt) REVERT: B 485 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7538 (mm-30) outliers start: 28 outliers final: 19 residues processed: 136 average time/residue: 0.1731 time to fit residues: 31.8713 Evaluate side-chains 129 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN A 591 GLN B 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 6548 Z= 0.438 Angle : 0.664 6.634 8926 Z= 0.347 Chirality : 0.048 0.152 1118 Planarity : 0.004 0.040 1084 Dihedral : 7.664 56.413 974 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.75 % Favored : 90.14 % Rotamer: Outliers : 5.39 % Allowed : 16.84 % Favored : 77.78 % 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: -3.41 (0.26), residues: 872 helix: -1.57 (0.20), residues: 610 sheet: None (None), residues: 0 loop : -3.73 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 714 HIS 0.004 0.003 HIS B 695 PHE 0.030 0.002 PHE A 590 TYR 0.007 0.002 TYR B 468 ARG 0.005 0.001 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 0.685 Fit side-chains REVERT: A 463 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8592 (mttt) REVERT: A 485 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 485 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7741 (mm-30) outliers start: 32 outliers final: 28 residues processed: 120 average time/residue: 0.1796 time to fit residues: 28.6376 Evaluate side-chains 122 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6548 Z= 0.174 Angle : 0.517 6.066 8926 Z= 0.270 Chirality : 0.041 0.116 1118 Planarity : 0.004 0.042 1084 Dihedral : 6.736 55.981 974 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.55 % Allowed : 19.53 % Favored : 75.93 % 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: -2.75 (0.27), residues: 872 helix: -0.99 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -3.51 (0.30), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 714 HIS 0.001 0.001 HIS A 695 PHE 0.027 0.001 PHE A 590 TYR 0.004 0.001 TYR B 383 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.688 Fit side-chains REVERT: A 463 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8585 (mttt) REVERT: A 473 PHE cc_start: 0.9195 (t80) cc_final: 0.8805 (t80) REVERT: A 485 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 463 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8567 (mttt) REVERT: B 485 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7609 (mm-30) outliers start: 27 outliers final: 23 residues processed: 135 average time/residue: 0.1656 time to fit residues: 30.1310 Evaluate side-chains 134 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN A 591 GLN B 506 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6548 Z= 0.182 Angle : 0.522 6.795 8926 Z= 0.270 Chirality : 0.042 0.121 1118 Planarity : 0.004 0.042 1084 Dihedral : 6.471 54.793 974 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.38 % Allowed : 20.20 % Favored : 75.42 % 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: -2.39 (0.28), residues: 872 helix: -0.70 (0.22), residues: 586 sheet: None (None), residues: 0 loop : -3.40 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 714 HIS 0.001 0.001 HIS A 695 PHE 0.023 0.001 PHE A 590 TYR 0.014 0.001 TYR A 748 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.737 Fit side-chains REVERT: A 473 PHE cc_start: 0.9159 (t80) cc_final: 0.8798 (t80) REVERT: A 485 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7638 (mm-30) REVERT: B 473 PHE cc_start: 0.9169 (t80) cc_final: 0.8778 (t80) REVERT: B 485 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7647 (mm-30) outliers start: 26 outliers final: 21 residues processed: 132 average time/residue: 0.1750 time to fit residues: 30.9326 Evaluate side-chains 129 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6548 Z= 0.216 Angle : 0.535 6.991 8926 Z= 0.277 Chirality : 0.042 0.125 1118 Planarity : 0.004 0.041 1084 Dihedral : 6.512 58.969 974 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.05 % Allowed : 20.71 % Favored : 74.24 % 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: -2.32 (0.28), residues: 872 helix: -0.66 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.47 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 714 HIS 0.001 0.001 HIS A 695 PHE 0.022 0.001 PHE B 590 TYR 0.014 0.001 TYR B 748 ARG 0.002 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.745 Fit side-chains REVERT: A 473 PHE cc_start: 0.9143 (t80) cc_final: 0.8788 (t80) REVERT: A 485 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 473 PHE cc_start: 0.9165 (t80) cc_final: 0.8776 (t80) REVERT: B 485 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7601 (mm-30) outliers start: 30 outliers final: 26 residues processed: 132 average time/residue: 0.1707 time to fit residues: 30.9504 Evaluate side-chains 130 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6548 Z= 0.166 Angle : 0.519 7.392 8926 Z= 0.267 Chirality : 0.041 0.122 1118 Planarity : 0.004 0.042 1084 Dihedral : 6.086 53.662 974 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.38 % Allowed : 22.22 % Favored : 73.40 % 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: -2.06 (0.28), residues: 872 helix: -0.45 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.39 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.021 0.001 PHE B 590 TYR 0.007 0.001 TYR A 353 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.665 Fit side-chains REVERT: A 473 PHE cc_start: 0.9124 (t80) cc_final: 0.8779 (t80) REVERT: A 485 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7555 (mm-30) REVERT: B 473 PHE cc_start: 0.9120 (t80) cc_final: 0.8733 (t80) REVERT: B 485 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7567 (mm-30) outliers start: 26 outliers final: 23 residues processed: 132 average time/residue: 0.1952 time to fit residues: 35.2177 Evaluate side-chains 127 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.0050 chunk 74 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6548 Z= 0.155 Angle : 0.516 7.443 8926 Z= 0.264 Chirality : 0.041 0.125 1118 Planarity : 0.004 0.041 1084 Dihedral : 5.857 55.065 974 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.38 % Allowed : 22.22 % Favored : 73.40 % 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: -1.81 (0.29), residues: 872 helix: -0.27 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.26 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 714 HIS 0.001 0.001 HIS B 695 PHE 0.022 0.001 PHE B 590 TYR 0.005 0.001 TYR B 353 ARG 0.004 0.000 ARG A 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.825 Fit side-chains REVERT: A 473 PHE cc_start: 0.9081 (t80) cc_final: 0.8725 (t80) REVERT: A 485 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 619 LEU cc_start: 0.9081 (tp) cc_final: 0.8873 (tt) REVERT: B 473 PHE cc_start: 0.9095 (t80) cc_final: 0.8715 (t80) REVERT: B 485 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 619 LEU cc_start: 0.9068 (tp) cc_final: 0.8857 (tt) outliers start: 26 outliers final: 24 residues processed: 138 average time/residue: 0.1832 time to fit residues: 34.5692 Evaluate side-chains 137 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 739 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN ** B 591 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 = 0.3536 r_free = 0.3536 target = 0.130807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104475 restraints weight = 8641.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107408 restraints weight = 4837.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109243 restraints weight = 3504.394| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6548 Z= 0.180 Angle : 0.523 7.465 8926 Z= 0.267 Chirality : 0.042 0.127 1118 Planarity : 0.004 0.041 1084 Dihedral : 5.909 57.052 974 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.21 % Allowed : 22.05 % Favored : 73.74 % 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: -1.70 (0.29), residues: 872 helix: -0.16 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.29 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 714 HIS 0.001 0.001 HIS B 695 PHE 0.020 0.001 PHE B 590 TYR 0.006 0.001 TYR A 353 ARG 0.004 0.001 ARG A 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1477.78 seconds wall clock time: 27 minutes 46.37 seconds (1666.37 seconds total)