Starting phenix.real_space_refine on Wed May 14 01:33:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dth_27698/05_2025/8dth_27698.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dth_27698/05_2025/8dth_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/cci-nas-00/data/ceres_data/8dth_27698/05_2025/8dth_27698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dth_27698/05_2025/8dth_27698.map" model { file = "/net/cci-nas-00/data/ceres_data/8dth_27698/05_2025/8dth_27698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dth_27698/05_2025/8dth_27698.cif" } 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. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.83, per 1000 atoms: 0.70 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.5 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: 1.55 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: 3.74 Time building geometry restraints manager: 3.36 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: 0.00 - 1.94: 15280 1.94 - 3.87: 228 3.87 - 5.81: 26 5.81 - 7.74: 3 7.74 - 9.68: 1 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 3.040 nonbonded pdb=" O MET A 238 " pdb=" OG1 THR A 241 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASN B 442 " pdb=" OH TYR B 594 " model vdw 2.295 3.040 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 Time spend for trying shortcut: 0.00 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.240 Find NCS groups from input model: 0.490 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- 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= 0.154 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 Details of bonding type rmsd hydrogen bonds : bond 0.11880 ( 697) hydrogen bonds : angle 5.44687 ( 2070) covalent geometry : bond 0.00341 (11416) covalent geometry : angle 0.60439 (15538) *********************** 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 to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.293 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: 0.1879 time to fit residues: 38.4831 Evaluate side-chains 97 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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: 2.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 662 ASN B 201 GLN B 367 ASN B 402 ASN B 442 ASN B 730 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089424 restraints weight = 25505.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088979 restraints weight = 14186.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088736 restraints weight = 12316.339| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11416 Z= 0.197 Angle : 0.586 10.033 15538 Z= 0.301 Chirality : 0.041 0.179 1745 Planarity : 0.005 0.052 1993 Dihedral : 3.857 15.933 1571 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.68 % Allowed : 4.73 % Favored : 94.60 % 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: 1.52 (0.23), residues: 1433 helix: 1.99 (0.17), residues: 949 sheet: -0.72 (0.47), residues: 131 loop : -0.98 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 591 HIS 0.006 0.001 HIS A 467 PHE 0.028 0.002 PHE A 829 TYR 0.019 0.002 TYR A 793 ARG 0.004 0.001 ARG A 838 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 697) hydrogen bonds : angle 4.25833 ( 2070) covalent geometry : bond 0.00459 (11416) covalent geometry : angle 0.58553 (15538) *********************** 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 111 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 489 SER cc_start: 0.9448 (t) cc_final: 0.8656 (m) REVERT: B 580 MET cc_start: 0.8582 (mmp) cc_final: 0.8081 (mmp) REVERT: B 730 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8027 (tp40) outliers start: 8 outliers final: 6 residues processed: 105 average time/residue: 0.1977 time to fit residues: 31.5033 Evaluate side-chains 99 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 567 GLU 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 48 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.123958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087513 restraints weight = 25701.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089581 restraints weight = 15316.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089891 restraints weight = 11433.567| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1541 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= 0.119 Angle : 0.495 8.007 15538 Z= 0.254 Chirality : 0.039 0.146 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.772 16.033 1571 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.01 % Allowed : 5.99 % Favored : 93.00 % 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: 2.14 (0.23), residues: 1433 helix: 2.39 (0.17), residues: 955 sheet: -0.52 (0.48), residues: 131 loop : -0.59 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.003 0.001 HIS A 726 PHE 0.022 0.001 PHE A 829 TYR 0.016 0.001 TYR B 732 ARG 0.003 0.000 ARG B 811 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 697) hydrogen bonds : angle 3.74748 ( 2070) covalent geometry : bond 0.00267 (11416) covalent geometry : angle 0.49487 (15538) *********************** 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 119 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.258 Fit side-chains REVERT: A 489 SER cc_start: 0.9423 (t) cc_final: 0.8719 (m) REVERT: B 192 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8862 (mt) REVERT: B 211 LYS cc_start: 0.8972 (mttt) cc_final: 0.8599 (mtpp) REVERT: B 580 MET cc_start: 0.8513 (mmp) cc_final: 0.8169 (mmm) outliers start: 12 outliers final: 5 residues processed: 113 average time/residue: 0.1974 time to fit residues: 34.4084 Evaluate side-chains 100 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 728 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 346 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 86 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 92 optimal weight: 0.2980 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.123236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088372 restraints weight = 25478.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088509 restraints weight = 15338.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088976 restraints weight = 11844.788| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1804 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= 0.132 Angle : 0.512 13.079 15538 Z= 0.257 Chirality : 0.040 0.212 1745 Planarity : 0.004 0.059 1993 Dihedral : 3.763 14.787 1571 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.10 % Allowed : 7.51 % 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: 2.21 (0.23), residues: 1433 helix: 2.42 (0.17), residues: 956 sheet: -0.43 (0.47), residues: 130 loop : -0.49 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 841 HIS 0.003 0.001 HIS A 508 PHE 0.020 0.001 PHE A 829 TYR 0.015 0.001 TYR A 793 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 697) hydrogen bonds : angle 3.61227 ( 2070) covalent geometry : bond 0.00302 (11416) covalent geometry : angle 0.51195 (15538) *********************** 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 111 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.451 Fit side-chains REVERT: A 489 SER cc_start: 0.9393 (t) cc_final: 0.8727 (m) REVERT: B 192 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8858 (mt) REVERT: B 580 MET cc_start: 0.8462 (mmp) cc_final: 0.8005 (mmm) REVERT: B 635 TYR cc_start: 0.6353 (t80) cc_final: 0.5703 (t80) REVERT: B 818 MET cc_start: 0.8836 (ttm) cc_final: 0.8604 (ppp) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.1888 time to fit residues: 30.9531 Evaluate side-chains 107 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 569 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 140 optimal weight: 0.0470 chunk 139 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.0470 chunk 97 optimal weight: 0.3980 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 588 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 = 0.3838 r_free = 0.3838 target = 0.124354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089532 restraints weight = 25303.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090086 restraints weight = 16291.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090039 restraints weight = 11726.307| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11416 Z= 0.099 Angle : 0.479 12.160 15538 Z= 0.240 Chirality : 0.038 0.180 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.656 14.921 1571 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.35 % Allowed : 8.10 % Favored : 90.55 % 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: 2.47 (0.23), residues: 1433 helix: 2.60 (0.17), residues: 955 sheet: -0.34 (0.47), residues: 130 loop : -0.36 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 461 HIS 0.003 0.001 HIS A 768 PHE 0.017 0.001 PHE A 829 TYR 0.012 0.001 TYR A 793 ARG 0.002 0.000 ARG B 676 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 697) hydrogen bonds : angle 3.41277 ( 2070) covalent geometry : bond 0.00218 (11416) covalent geometry : angle 0.47944 (15538) *********************** 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 120 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.108 Fit side-chains REVERT: A 200 MET cc_start: 0.8613 (mpp) cc_final: 0.8332 (mpp) REVERT: A 253 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8227 (t80) REVERT: A 483 ILE cc_start: 0.7802 (mt) cc_final: 0.7602 (tt) REVERT: A 489 SER cc_start: 0.9404 (t) cc_final: 0.8833 (m) REVERT: A 491 ASP cc_start: 0.8379 (m-30) cc_final: 0.8154 (m-30) REVERT: B 192 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B 580 MET cc_start: 0.8372 (mmp) cc_final: 0.7939 (mmm) REVERT: B 635 TYR cc_start: 0.6362 (t80) cc_final: 0.5734 (t80) REVERT: B 818 MET cc_start: 0.8909 (ttm) cc_final: 0.8683 (ppp) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.1746 time to fit residues: 31.3769 Evaluate side-chains 106 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 597 THR 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 76 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 79 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088481 restraints weight = 25760.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088024 restraints weight = 14539.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087835 restraints weight = 12812.866| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2090 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= 0.146 Angle : 0.518 15.122 15538 Z= 0.257 Chirality : 0.039 0.156 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.682 14.605 1571 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.27 % Allowed : 8.61 % Favored : 90.13 % 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: 2.48 (0.23), residues: 1433 helix: 2.63 (0.17), residues: 956 sheet: -0.38 (0.46), residues: 130 loop : -0.39 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 461 HIS 0.005 0.001 HIS A 508 PHE 0.019 0.001 PHE A 829 TYR 0.016 0.001 TYR A 793 ARG 0.003 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 697) hydrogen bonds : angle 3.48490 ( 2070) covalent geometry : bond 0.00338 (11416) covalent geometry : angle 0.51821 (15538) *********************** 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 to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.8606 (mpp) cc_final: 0.8331 (mpp) REVERT: A 489 SER cc_start: 0.9373 (t) cc_final: 0.8822 (m) REVERT: A 491 ASP cc_start: 0.8436 (m-30) cc_final: 0.8235 (m-30) REVERT: B 192 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8895 (mt) REVERT: B 219 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: B 580 MET cc_start: 0.8490 (mmp) cc_final: 0.8008 (mmm) REVERT: B 635 TYR cc_start: 0.6380 (t80) cc_final: 0.5826 (t80) REVERT: B 729 MET cc_start: 0.7472 (mmm) cc_final: 0.7226 (tmm) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.2163 time to fit residues: 35.8180 Evaluate side-chains 109 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 597 THR 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 219 TYR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.0270 chunk 11 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086106 restraints weight = 25698.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087803 restraints weight = 16024.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088554 restraints weight = 11745.387| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2192 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= 0.109 Angle : 0.509 13.900 15538 Z= 0.248 Chirality : 0.039 0.147 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.677 14.920 1571 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.10 % Allowed : 9.54 % Favored : 89.37 % 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: 2.60 (0.23), residues: 1433 helix: 2.73 (0.17), residues: 955 sheet: -0.32 (0.47), residues: 130 loop : -0.37 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 461 HIS 0.003 0.001 HIS A 508 PHE 0.017 0.001 PHE A 829 TYR 0.014 0.001 TYR A 793 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 697) hydrogen bonds : angle 3.39896 ( 2070) covalent geometry : bond 0.00249 (11416) covalent geometry : angle 0.50917 (15538) *********************** 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 112 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8641 (ptt) cc_final: 0.8246 (ptt) REVERT: A 200 MET cc_start: 0.8639 (mpp) cc_final: 0.8260 (mpp) REVERT: A 489 SER cc_start: 0.9377 (t) cc_final: 0.8828 (m) REVERT: A 491 ASP cc_start: 0.8394 (m-30) cc_final: 0.8181 (m-30) REVERT: B 192 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8858 (mt) REVERT: B 219 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: B 580 MET cc_start: 0.8425 (mmp) cc_final: 0.7960 (mmm) REVERT: B 635 TYR cc_start: 0.6567 (t80) cc_final: 0.5740 (t80) REVERT: B 729 MET cc_start: 0.7468 (mmm) cc_final: 0.7248 (tmm) REVERT: B 818 MET cc_start: 0.8945 (ppp) cc_final: 0.8063 (ptm) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.1888 time to fit residues: 31.3824 Evaluate side-chains 109 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 597 THR 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 219 TYR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 134 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 126 optimal weight: 0.0370 chunk 1 optimal weight: 20.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 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 = 0.3817 r_free = 0.3817 target = 0.123066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087803 restraints weight = 25544.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088056 restraints weight = 16591.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.088891 restraints weight = 11975.256| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2293 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= 0.118 Angle : 0.510 13.500 15538 Z= 0.252 Chirality : 0.039 0.141 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.667 14.897 1571 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.43 % Allowed : 9.45 % Favored : 89.11 % 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: 2.78 (0.17), residues: 953 sheet: -0.17 (0.49), residues: 119 loop : -0.43 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 461 HIS 0.003 0.001 HIS A 508 PHE 0.017 0.001 PHE A 829 TYR 0.014 0.001 TYR A 793 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 697) hydrogen bonds : angle 3.38375 ( 2070) covalent geometry : bond 0.00271 (11416) covalent geometry : angle 0.51007 (15538) *********************** 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 119 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8650 (ptt) cc_final: 0.8208 (ptt) REVERT: A 200 MET cc_start: 0.8624 (mpp) cc_final: 0.8248 (mpp) REVERT: A 253 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8237 (t80) REVERT: A 489 SER cc_start: 0.9369 (t) cc_final: 0.8822 (m) REVERT: B 192 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8853 (mt) REVERT: B 219 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: B 580 MET cc_start: 0.8416 (mmp) cc_final: 0.7946 (mmm) REVERT: B 735 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7842 (ttp) REVERT: B 818 MET cc_start: 0.8995 (ppp) cc_final: 0.8638 (ppp) outliers start: 17 outliers final: 12 residues processed: 110 average time/residue: 0.1918 time to fit residues: 32.6830 Evaluate side-chains 110 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 597 THR 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 219 TYR Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN B 225 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.088924 restraints weight = 25671.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089048 restraints weight = 14846.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088536 restraints weight = 12847.615| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 0.029 11416 Z= 0.110 Angle : 0.513 12.668 15538 Z= 0.253 Chirality : 0.039 0.136 1745 Planarity : 0.004 0.059 1993 Dihedral : 3.644 14.995 1571 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.35 % Allowed : 10.46 % Favored : 88.19 % 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: 2.67 (0.23), residues: 1433 helix: 2.77 (0.17), residues: 960 sheet: -0.05 (0.50), residues: 119 loop : -0.46 (0.35), residues: 354 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 0.017 0.001 PHE A 829 TYR 0.013 0.001 TYR A 793 ARG 0.002 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 697) hydrogen bonds : angle 3.36316 ( 2070) covalent geometry : bond 0.00251 (11416) covalent geometry : angle 0.51264 (15538) *********************** 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 109 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8670 (ptt) cc_final: 0.8228 (ptt) REVERT: A 200 MET cc_start: 0.8659 (mpp) cc_final: 0.8285 (mpp) REVERT: A 253 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8234 (t80) REVERT: A 489 SER cc_start: 0.9389 (t) cc_final: 0.8832 (m) REVERT: B 192 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8875 (mt) REVERT: B 219 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: B 580 MET cc_start: 0.8461 (mmp) cc_final: 0.7981 (mmm) REVERT: B 735 MET cc_start: 0.8332 (ptp) cc_final: 0.7900 (ttp) REVERT: B 818 MET cc_start: 0.8955 (ppp) cc_final: 0.8498 (ppp) outliers start: 16 outliers final: 12 residues processed: 101 average time/residue: 0.1995 time to fit residues: 31.4567 Evaluate side-chains 107 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 597 THR 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 219 TYR Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 31 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- 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** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087312 restraints weight = 25748.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089328 restraints weight = 15585.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089600 restraints weight = 11833.642| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2476 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= 0.098 Angle : 0.510 12.927 15538 Z= 0.250 Chirality : 0.038 0.141 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.607 15.979 1571 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.35 % Allowed : 10.30 % Favored : 88.35 % 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: 2.70 (0.23), residues: 1433 helix: 2.79 (0.17), residues: 957 sheet: -0.01 (0.50), residues: 119 loop : -0.42 (0.35), residues: 357 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 0.015 0.001 PHE A 829 TYR 0.012 0.001 TYR A 793 ARG 0.002 0.000 ARG B 676 Details of bonding type rmsd hydrogen bonds : bond 0.02655 ( 697) hydrogen bonds : angle 3.30960 ( 2070) covalent geometry : bond 0.00221 (11416) covalent geometry : angle 0.51047 (15538) ********************** 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 113 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8670 (ptt) cc_final: 0.8269 (ptt) REVERT: A 200 MET cc_start: 0.8651 (mpp) cc_final: 0.8322 (mpp) REVERT: A 253 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8219 (t80) REVERT: A 489 SER cc_start: 0.9394 (t) cc_final: 0.8818 (m) REVERT: A 501 ILE cc_start: 0.9067 (tp) cc_final: 0.8864 (tp) REVERT: B 192 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8831 (mt) REVERT: B 219 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: B 580 MET cc_start: 0.8429 (mmp) cc_final: 0.7989 (mmm) REVERT: B 735 MET cc_start: 0.8339 (ptp) cc_final: 0.7922 (ttp) outliers start: 16 outliers final: 11 residues processed: 107 average time/residue: 0.1936 time to fit residues: 31.7611 Evaluate side-chains 105 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 508 HIS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 597 THR 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 219 TYR Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 24 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 128 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086775 restraints weight = 25470.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088403 restraints weight = 15873.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089291 restraints weight = 11739.639| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2518 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= 0.108 Angle : 0.517 11.996 15538 Z= 0.255 Chirality : 0.039 0.130 1745 Planarity : 0.004 0.058 1993 Dihedral : 3.616 15.486 1571 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.18 % Allowed : 10.63 % Favored : 88.19 % 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: 2.70 (0.23), residues: 1433 helix: 2.80 (0.17), residues: 957 sheet: -0.04 (0.50), residues: 119 loop : -0.46 (0.35), residues: 357 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 0.015 0.001 PHE A 829 TYR 0.017 0.001 TYR B 755 ARG 0.009 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 697) hydrogen bonds : angle 3.32951 ( 2070) covalent geometry : bond 0.00247 (11416) covalent geometry : angle 0.51717 (15538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.44 seconds wall clock time: 58 minutes 14.46 seconds (3494.46 seconds total)