Starting phenix.real_space_refine on Thu Feb 15 04:47:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dth_27698/02_2024/8dth_27698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dth_27698/02_2024/8dth_27698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dth_27698/02_2024/8dth_27698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dth_27698/02_2024/8dth_27698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dth_27698/02_2024/8dth_27698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dth_27698/02_2024/8dth_27698.pdb" } resolution = 3.6 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= 1.000 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 88 5.16 5 C 7126 2.51 5 N 1848 2.21 5 O 2091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "B GLU 398": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11153 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5732 Classifications: {'peptide': 736} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 701} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5421 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 667} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 6.32, per 1000 atoms: 0.57 Number of scatterers: 11153 At special positions: 0 Unit cell: (97.68, 101.2, 160.16, 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 88 16.00 O 2091 8.00 N 1848 7.00 C 7126 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: 4.65 Conformation dependent library (CDL) restraints added in 2.2 seconds 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 4 sheets defined 69.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.531A pdb=" N GLU A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.696A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.852A pdb=" N TYR A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.803A pdb=" N TYR A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 Processing helix chain 'A' and resid 253 through 274 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.539A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.521A pdb=" N GLU A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 508 removed outlier: 5.161A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.523A pdb=" N CYS A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 removed outlier: 4.001A pdb=" N SER A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 681 Processing helix chain 'A' and resid 691 through 694 removed outlier: 3.907A pdb=" N CYS A 694 " --> pdb=" O LYS A 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 695 through 709 removed outlier: 3.589A pdb=" N LEU A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 732 through 735 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 767 through 781 removed outlier: 5.294A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.754A pdb=" N ASP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 removed outlier: 4.465A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 824 Processing helix chain 'A' and resid 825 through 846 Processing helix chain 'B' and resid 147 through 165 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.599A pdb=" N TYR B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 236 through 250 Processing helix chain 'B' and resid 253 through 275 Processing helix chain 'B' and resid 276 through 291 removed outlier: 3.541A pdb=" N TYR B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 309 Processing helix chain 'B' and resid 310 through 325 Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.708A pdb=" N TYR B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 Processing helix chain 'B' and resid 497 through 507 removed outlier: 5.238A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 647 through 653 removed outlier: 3.684A pdb=" N SER B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 667 through 681 removed outlier: 3.763A pdb=" N VAL B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 694 Processing helix chain 'B' and resid 695 through 710 removed outlier: 3.566A pdb=" N ARG B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 732 through 735 removed outlier: 3.653A pdb=" N MET B 735 " --> pdb=" O TYR B 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 767 through 781 removed outlier: 5.173A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 789 through 803 removed outlier: 3.633A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 820 removed outlier: 4.222A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 824 Processing helix chain 'B' and resid 825 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544 removed outlier: 8.803A pdb=" N VAL A 541 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 515 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS A 543 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 517 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 483 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 516 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 485 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N TYR A 518 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 487 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 484 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL A 566 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 486 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN A 588 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE A 607 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR A 590 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ASP A 609 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719 removed outlier: 6.406A pdb=" N LEU A 686 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 719 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 688 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 656 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU A 739 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY A 658 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER A 738 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N MET A 763 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA A 787 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 762 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 541 through 544 removed outlier: 6.262A pdb=" N ILE B 483 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 516 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 485 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR B 518 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR B 487 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 484 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL B 566 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY B 486 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN B 588 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 607 " --> pdb=" O GLN B 588 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 590 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N ASP B 609 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 716 through 719 removed outlier: 8.165A pdb=" N ASP B 717 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 686 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 719 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 688 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR B 656 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 739 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY B 658 " --> pdb=" O LEU B 739 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER B 738 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N MET B 763 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA B 787 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR B 762 " --> pdb=" O ALA B 787 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 2070 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: 3.84 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3598 1.34 - 1.46: 2113 1.46 - 1.58: 5573 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 11416 Sorted by residual: bond pdb=" CB PRO A 743 " pdb=" CG PRO A 743 " ideal model delta sigma weight residual 1.506 1.463 0.043 3.90e-02 6.57e+02 1.24e+00 bond pdb=" CG PRO A 692 " pdb=" CD PRO A 692 " ideal model delta sigma weight residual 1.503 1.473 0.030 3.40e-02 8.65e+02 7.99e-01 bond pdb=" CG1 ILE A 677 " pdb=" CD1 ILE A 677 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.35e-01 bond pdb=" CB PRO B 743 " pdb=" CG PRO B 743 " ideal model delta sigma weight residual 1.506 1.473 0.033 3.90e-02 6.57e+02 7.12e-01 bond pdb=" CA TRP A 459 " pdb=" C TRP A 459 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.29e-02 6.01e+03 6.99e-01 ... (remaining 11411 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.30: 342 106.30 - 113.23: 6101 113.23 - 120.17: 4313 120.17 - 127.11: 4655 127.11 - 134.04: 127 Bond angle restraints: 15538 Sorted by residual: angle pdb=" CA LEU B 734 " pdb=" CB LEU B 734 " pdb=" CG LEU B 734 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 angle pdb=" N GLU A 350 " pdb=" CA GLU A 350 " pdb=" CB GLU A 350 " ideal model delta sigma weight residual 110.12 114.09 -3.97 1.47e+00 4.63e-01 7.31e+00 angle pdb=" N PHE A 463 " pdb=" CA PHE A 463 " pdb=" CB PHE A 463 " ideal model delta sigma weight residual 110.16 106.48 3.68 1.48e+00 4.57e-01 6.19e+00 angle pdb=" N TRP B 591 " pdb=" CA TRP B 591 " pdb=" C TRP B 591 " ideal model delta sigma weight residual 110.80 116.05 -5.25 2.13e+00 2.20e-01 6.08e+00 angle pdb=" N LYS A 691 " pdb=" CA LYS A 691 " pdb=" C LYS A 691 " ideal model delta sigma weight residual 113.57 116.74 -3.17 1.38e+00 5.25e-01 5.27e+00 ... (remaining 15533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 6305 17.24 - 34.48: 413 34.48 - 51.72: 90 51.72 - 68.97: 10 68.97 - 86.21: 5 Dihedral angle restraints: 6823 sinusoidal: 2589 harmonic: 4234 Sorted by residual: dihedral pdb=" CA VAL A 589 " pdb=" C VAL A 589 " pdb=" N THR A 590 " pdb=" CA THR A 590 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA THR A 506 " pdb=" C THR A 506 " pdb=" N HIS A 507 " pdb=" CA HIS A 507 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CG ARG A 685 " pdb=" CD ARG A 685 " pdb=" NE ARG A 685 " pdb=" CZ ARG A 685 " ideal model delta sinusoidal sigma weight residual -90.00 -134.62 44.62 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 6820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1343 0.042 - 0.085: 293 0.085 - 0.127: 100 0.127 - 0.170: 7 0.170 - 0.212: 2 Chirality restraints: 1745 Sorted by residual: chirality pdb=" CB THR A 464 " pdb=" CA THR A 464 " pdb=" OG1 THR A 464 " pdb=" CG2 THR A 464 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL B 716 " pdb=" N VAL B 716 " pdb=" C VAL B 716 " pdb=" CB VAL B 716 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" C PRO A 479 " pdb=" CB PRO A 479 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1742 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 427 " 0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO B 428 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 250 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO A 251 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 145 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 146 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.036 5.00e-02 4.00e+02 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 995 2.74 - 3.28: 12189 3.28 - 3.82: 19446 3.82 - 4.36: 23021 4.36 - 4.90: 38825 Nonbonded interactions: 94476 Sorted by model distance: nonbonded pdb=" O ASP A 346 " pdb=" OE1 GLU A 350 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR B 635 " pdb=" OE2 GLU B 752 " model vdw 2.261 2.440 nonbonded pdb=" O MET A 238 " pdb=" OG1 THR A 241 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASN B 442 " pdb=" OH TYR B 594 " model vdw 2.295 2.440 nonbonded pdb=" O PRO A 682 " pdb=" OD1 ASN A 683 " model vdw 2.313 3.040 ... (remaining 94471 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' and (resid 146 through 154 or (resid 155 and (name N or name CA or na \ me C or name O or name CB )) or resid 156 through 179 or (resid 180 and (name N \ or name CA or name C or name O or name CB )) or resid 181 through 195 or (resid \ 196 and (name N or name CA or name C or name O or name CB )) or resid 197 throug \ h 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or \ resid 219 through 285 or (resid 286 through 287 and (name N or name CA or name C \ or name O or name CB )) or resid 288 through 386 or (resid 387 and (name N or n \ ame CA or name C or name O or name CB )) or resid 388 through 447 or (resid 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 through 46 \ 1 or (resid 462 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 through 511 or (resid 512 and (name N or name CA or name C or name O or na \ me CB )) or resid 513 or (resid 514 and (name N or name CA or name C or name O o \ r name CB )) or resid 515 through 522 or (resid 523 through 524 and (name N or n \ ame CA or name C or name O or name CB )) or resid 525 through 542 or (resid 543 \ and (name N or name CA or name C or name O or name CB )) or resid 544 through 56 \ 6 or (resid 567 and (name N or name CA or name C or name O or name CB )) or resi \ d 568 through 668 or (resid 669 and (name N or name CA or name C or name O or na \ me CB )) or resid 670 through 722 or (resid 723 and (name N or name CA or name C \ or name O or name CB )) or resid 724 through 794 or (resid 795 and (name N or n \ ame CA or name C or name O or name CB )) or resid 796 through 815 or (resid 816 \ and (name N or name CA or name C or name O or name CB )) or resid 817 through 83 \ 7 or (resid 838 and (name N or name CA or name C or name O or name CB )) or resi \ d 839 or (resid 840 and (name N or name CA or name C or name O or name CB )) or \ resid 841 through 846)) selection = (chain 'B' and (resid 146 through 414 or (resid 415 through 416 and (name N or n \ ame CA or name C or name O or name CB )) or resid 417 through 420 or (resid 421 \ and (name N or name CA or name C or name O or name CB )) or resid 422 through 42 \ 8 or (resid 429 and (name N or name CA or name C or name O or name CB )) or resi \ d 430 through 706 or (resid 707 and (name N or name CA or name C or name O or na \ me CB )) or resid 708 through 846)) } 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: 5.660 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: 0.020 Extract box with map and model: 12.290 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.310 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11416 Z= 0.218 Angle : 0.604 9.678 15538 Z= 0.324 Chirality : 0.041 0.212 1745 Planarity : 0.006 0.078 1993 Dihedral : 12.279 86.208 4113 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 (0.22), residues: 1433 helix: 0.80 (0.16), residues: 945 sheet: -0.83 (0.50), residues: 121 loop : -1.98 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 841 HIS 0.005 0.001 HIS A 508 PHE 0.040 0.003 PHE A 829 TYR 0.034 0.002 TYR A 134 ARG 0.008 0.001 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 553 ILE cc_start: 0.8808 (mm) cc_final: 0.8339 (mm) REVERT: B 211 LYS cc_start: 0.9125 (mttm) cc_final: 0.8760 (mttt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1916 time to fit residues: 38.9717 Evaluate side-chains 97 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0870 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 662 ASN B 201 GLN B 367 ASN B 402 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11416 Z= 0.205 Angle : 0.548 10.686 15538 Z= 0.279 Chirality : 0.040 0.180 1745 Planarity : 0.005 0.050 1993 Dihedral : 3.815 16.567 1571 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.59 % Allowed : 4.98 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.68 (0.23), residues: 1433 helix: 2.10 (0.17), residues: 950 sheet: -0.67 (0.47), residues: 131 loop : -0.92 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 841 HIS 0.005 0.001 HIS A 726 PHE 0.027 0.002 PHE A 829 TYR 0.019 0.002 TYR A 134 ARG 0.004 0.001 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 SER cc_start: 0.9463 (t) cc_final: 0.8882 (m) REVERT: A 491 ASP cc_start: 0.8463 (m-30) cc_final: 0.8207 (m-30) REVERT: B 580 MET cc_start: 0.8612 (mmp) cc_final: 0.8076 (mmp) REVERT: B 729 MET cc_start: 0.7427 (mmm) cc_final: 0.7221 (mmm) REVERT: B 730 GLN cc_start: 0.8092 (tp40) cc_final: 0.7843 (tp40) outliers start: 7 outliers final: 5 residues processed: 109 average time/residue: 0.2098 time to fit residues: 34.5187 Evaluate side-chains 101 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 346 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 662 ASN B 825 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11416 Z= 0.188 Angle : 0.491 8.109 15538 Z= 0.252 Chirality : 0.039 0.141 1745 Planarity : 0.004 0.054 1993 Dihedral : 3.718 14.997 1571 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.01 % Allowed : 5.91 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.19 (0.23), residues: 1433 helix: 2.47 (0.17), residues: 948 sheet: -0.49 (0.47), residues: 131 loop : -0.64 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 841 HIS 0.004 0.001 HIS A 508 PHE 0.022 0.001 PHE A 829 TYR 0.016 0.001 TYR A 793 ARG 0.003 0.000 ARG B 676 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 489 SER cc_start: 0.9434 (t) cc_final: 0.8878 (m) REVERT: A 491 ASP cc_start: 0.8498 (m-30) cc_final: 0.8270 (m-30) REVERT: B 192 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8856 (mt) REVERT: B 211 LYS cc_start: 0.8839 (mttt) cc_final: 0.8417 (mtpp) REVERT: B 580 MET cc_start: 0.8616 (mmp) cc_final: 0.8079 (mmm) REVERT: B 730 GLN cc_start: 0.8083 (tp40) cc_final: 0.7723 (tp40) outliers start: 12 outliers final: 4 residues processed: 109 average time/residue: 0.2016 time to fit residues: 33.6591 Evaluate side-chains 99 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 496 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 402 ASN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11416 Z= 0.186 Angle : 0.496 13.247 15538 Z= 0.248 Chirality : 0.039 0.183 1745 Planarity : 0.004 0.056 1993 Dihedral : 3.678 14.460 1571 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.35 % Allowed : 7.26 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.36 (0.23), residues: 1433 helix: 2.57 (0.17), residues: 950 sheet: -0.31 (0.47), residues: 130 loop : -0.55 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.003 0.001 HIS A 508 PHE 0.021 0.001 PHE A 829 TYR 0.015 0.001 TYR A 793 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.354 Fit side-chains REVERT: A 489 SER cc_start: 0.9414 (t) cc_final: 0.8898 (m) REVERT: A 491 ASP cc_start: 0.8518 (m-30) cc_final: 0.8274 (m-30) REVERT: B 192 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8866 (mt) REVERT: B 569 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7260 (t) REVERT: B 580 MET cc_start: 0.8649 (mmp) cc_final: 0.8096 (mmm) REVERT: B 730 GLN cc_start: 0.8102 (tp40) cc_final: 0.7722 (tp40) outliers start: 16 outliers final: 9 residues processed: 108 average time/residue: 0.2057 time to fit residues: 34.5831 Evaluate side-chains 107 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 569 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11416 Z= 0.139 Angle : 0.472 12.284 15538 Z= 0.237 Chirality : 0.038 0.138 1745 Planarity : 0.004 0.057 1993 Dihedral : 3.619 15.270 1571 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.10 % Allowed : 8.52 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.45 (0.23), residues: 1433 helix: 2.59 (0.17), residues: 962 sheet: -0.35 (0.48), residues: 122 loop : -0.43 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 841 HIS 0.003 0.001 HIS A 768 PHE 0.017 0.001 PHE A 829 TYR 0.013 0.001 TYR A 793 ARG 0.002 0.000 ARG B 676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 253 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8145 (t80) REVERT: A 489 SER cc_start: 0.9399 (t) cc_final: 0.8855 (m) REVERT: A 491 ASP cc_start: 0.8498 (m-30) cc_final: 0.8246 (m-30) REVERT: B 192 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8866 (mt) REVERT: B 569 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7280 (t) REVERT: B 580 MET cc_start: 0.8570 (mmp) cc_final: 0.8086 (mmm) REVERT: B 730 GLN cc_start: 0.8027 (tp40) cc_final: 0.7603 (tp40) outliers start: 13 outliers final: 6 residues processed: 112 average time/residue: 0.1930 time to fit residues: 33.1586 Evaluate side-chains 106 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 569 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11416 Z= 0.146 Angle : 0.471 11.974 15538 Z= 0.233 Chirality : 0.038 0.127 1745 Planarity : 0.004 0.057 1993 Dihedral : 3.568 15.502 1571 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.35 % Allowed : 9.03 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.56 (0.23), residues: 1433 helix: 2.67 (0.17), residues: 962 sheet: -0.31 (0.48), residues: 121 loop : -0.37 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 461 HIS 0.003 0.001 HIS A 768 PHE 0.017 0.001 PHE A 829 TYR 0.013 0.001 TYR A 793 ARG 0.002 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 253 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8175 (t80) REVERT: A 489 SER cc_start: 0.9385 (t) cc_final: 0.8878 (m) REVERT: A 491 ASP cc_start: 0.8490 (m-30) cc_final: 0.8244 (m-30) REVERT: B 192 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8846 (mt) REVERT: B 225 ASN cc_start: 0.7663 (m-40) cc_final: 0.7366 (m-40) REVERT: B 580 MET cc_start: 0.8536 (mmp) cc_final: 0.8065 (mmm) REVERT: B 730 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7597 (tp40) outliers start: 16 outliers final: 7 residues processed: 108 average time/residue: 0.1958 time to fit residues: 32.9425 Evaluate side-chains 104 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 346 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 0.0020 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 63 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11416 Z= 0.147 Angle : 0.475 12.156 15538 Z= 0.234 Chirality : 0.038 0.124 1745 Planarity : 0.004 0.057 1993 Dihedral : 3.558 15.489 1571 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.93 % Allowed : 9.62 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.65 (0.23), residues: 1433 helix: 2.73 (0.17), residues: 962 sheet: -0.23 (0.48), residues: 121 loop : -0.35 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 461 HIS 0.003 0.001 HIS A 768 PHE 0.016 0.001 PHE A 829 TYR 0.015 0.001 TYR B 219 ARG 0.002 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.8413 (mpp) cc_final: 0.8148 (mpp) REVERT: A 253 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8194 (t80) REVERT: A 489 SER cc_start: 0.9388 (t) cc_final: 0.8881 (m) REVERT: A 491 ASP cc_start: 0.8470 (m-30) cc_final: 0.8247 (m-30) REVERT: B 192 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8850 (mt) REVERT: B 219 TYR cc_start: 0.6889 (m-80) cc_final: 0.6467 (m-80) REVERT: B 450 ASP cc_start: 0.6747 (t70) cc_final: 0.6454 (t0) REVERT: B 580 MET cc_start: 0.8534 (mmp) cc_final: 0.8065 (mmm) REVERT: B 735 MET cc_start: 0.8144 (ptp) cc_final: 0.7763 (ttp) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 0.2018 time to fit residues: 32.3727 Evaluate side-chains 105 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN B 225 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11416 Z= 0.169 Angle : 0.487 12.038 15538 Z= 0.239 Chirality : 0.038 0.123 1745 Planarity : 0.004 0.057 1993 Dihedral : 3.561 15.571 1571 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 10.21 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.66 (0.23), residues: 1433 helix: 2.74 (0.17), residues: 964 sheet: 0.03 (0.51), residues: 110 loop : -0.49 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 461 HIS 0.003 0.001 HIS A 768 PHE 0.016 0.001 PHE A 829 TYR 0.014 0.001 TYR A 793 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.8411 (mpp) cc_final: 0.8063 (mpp) REVERT: A 489 SER cc_start: 0.9388 (t) cc_final: 0.8888 (m) REVERT: A 491 ASP cc_start: 0.8483 (m-30) cc_final: 0.8265 (m-30) REVERT: B 192 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8843 (mt) REVERT: B 450 ASP cc_start: 0.6767 (t70) cc_final: 0.6446 (t0) REVERT: B 580 MET cc_start: 0.8536 (mmp) cc_final: 0.8069 (mmm) REVERT: B 735 MET cc_start: 0.8217 (ptp) cc_final: 0.7870 (ttp) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.1942 time to fit residues: 31.6700 Evaluate side-chains 104 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 116 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11416 Z= 0.149 Angle : 0.493 12.230 15538 Z= 0.241 Chirality : 0.038 0.124 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.555 15.409 1571 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.93 % Allowed : 10.46 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.68 (0.23), residues: 1433 helix: 2.77 (0.17), residues: 964 sheet: -0.03 (0.51), residues: 110 loop : -0.46 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 461 HIS 0.003 0.001 HIS A 768 PHE 0.016 0.001 PHE A 829 TYR 0.014 0.001 TYR B 755 ARG 0.002 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.8376 (mpp) cc_final: 0.8044 (mpp) REVERT: A 253 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8224 (t80) REVERT: A 489 SER cc_start: 0.9389 (t) cc_final: 0.8870 (m) REVERT: A 491 ASP cc_start: 0.8477 (m-30) cc_final: 0.8248 (m-30) REVERT: B 192 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8835 (mt) REVERT: B 219 TYR cc_start: 0.7041 (m-80) cc_final: 0.6683 (m-80) REVERT: B 450 ASP cc_start: 0.6794 (t70) cc_final: 0.6464 (t0) REVERT: B 580 MET cc_start: 0.8510 (mmp) cc_final: 0.8054 (mmm) REVERT: B 735 MET cc_start: 0.8277 (ptp) cc_final: 0.7898 (ttp) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2039 time to fit residues: 31.4673 Evaluate side-chains 104 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 131 optimal weight: 0.0370 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11416 Z= 0.176 Angle : 0.512 11.944 15538 Z= 0.250 Chirality : 0.039 0.126 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.562 15.509 1571 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.01 % Allowed : 10.46 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.65 (0.23), residues: 1433 helix: 2.74 (0.17), residues: 971 sheet: 0.02 (0.54), residues: 99 loop : -0.57 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 461 HIS 0.003 0.001 HIS A 508 PHE 0.016 0.001 PHE A 829 TYR 0.020 0.001 TYR B 755 ARG 0.003 0.000 ARG A 838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2866 Ramachandran restraints generated. 1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.308 Fit side-chains REVERT: A 200 MET cc_start: 0.8359 (mpp) cc_final: 0.8037 (mpp) REVERT: A 253 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8246 (t80) REVERT: A 489 SER cc_start: 0.9391 (t) cc_final: 0.8872 (m) REVERT: A 491 ASP cc_start: 0.8494 (m-30) cc_final: 0.8263 (m-30) REVERT: B 192 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8839 (mt) REVERT: B 450 ASP cc_start: 0.6731 (t70) cc_final: 0.6377 (t0) REVERT: B 580 MET cc_start: 0.8514 (mmp) cc_final: 0.7992 (mmm) REVERT: B 613 ASP cc_start: 0.7552 (m-30) cc_final: 0.7299 (m-30) REVERT: B 735 MET cc_start: 0.8288 (ptp) cc_final: 0.7897 (ttp) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.1962 time to fit residues: 30.7773 Evaluate side-chains 104 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.0370 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 116 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 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 = 0.3832 r_free = 0.3832 target = 0.124016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090451 restraints weight = 25231.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.089992 restraints weight = 14566.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.089835 restraints weight = 13445.103| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11416 Z= 0.149 Angle : 0.498 12.178 15538 Z= 0.242 Chirality : 0.038 0.122 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.557 15.382 1571 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.01 % Allowed : 10.55 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.69 (0.23), residues: 1433 helix: 2.76 (0.17), residues: 972 sheet: 0.10 (0.55), residues: 99 loop : -0.55 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 461 HIS 0.003 0.001 HIS A 768 PHE 0.016 0.001 PHE A 829 TYR 0.015 0.001 TYR B 755 ARG 0.002 0.000 ARG A 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.79 seconds wall clock time: 39 minutes 45.97 seconds (2385.97 seconds total)