Starting phenix.real_space_refine on Wed Jun 11 16:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2h_47452/06_2025/9e2h_47452.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2h_47452/06_2025/9e2h_47452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2h_47452/06_2025/9e2h_47452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2h_47452/06_2025/9e2h_47452.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2h_47452/06_2025/9e2h_47452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2h_47452/06_2025/9e2h_47452.cif" } resolution = 2.77 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= 0.000 sd= 0.013 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 78 5.16 5 C 8219 2.51 5 N 2249 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2176 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Chain: "C" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2180 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 1 Chain: "D" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Chain: "E" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2166 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Time building chain proxies: 8.77, per 1000 atoms: 0.67 Number of scatterers: 13074 At special positions: 0 Unit cell: (128.52, 126.36, 77.76, 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 78 16.00 O 2528 8.00 N 2249 7.00 C 8219 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: 3.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3068 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 6 sheets defined 83.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.619A pdb=" N VAL A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 488 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 503 through 523 removed outlier: 3.568A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 527 through 555 removed outlier: 4.007A pdb=" N MET A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.773A pdb=" N GLN A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.546A pdb=" N GLN A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 619 Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 650 through 663 removed outlier: 3.603A pdb=" N ARG A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 679 Processing helix chain 'A' and resid 682 through 710 removed outlier: 3.577A pdb=" N GLU A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 461 through 486 removed outlier: 3.674A pdb=" N ILE B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 503 through 524 removed outlier: 3.763A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 554 removed outlier: 3.971A pdb=" N MET B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 535 " --> pdb=" O MET B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.505A pdb=" N THR B 571 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 Processing helix chain 'B' and resid 594 through 619 removed outlier: 3.663A pdb=" N LEU B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 removed outlier: 3.511A pdb=" N HIS B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 4.093A pdb=" N ARG B 654 " --> pdb=" O ASN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 Processing helix chain 'B' and resid 682 through 709 removed outlier: 3.936A pdb=" N TYR B 686 " --> pdb=" O GLY B 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 445 through 458 removed outlier: 3.767A pdb=" N VAL C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 4.043A pdb=" N ILE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 503 through 523 removed outlier: 3.520A pdb=" N LEU C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 523 " --> pdb=" O MET C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 526 No H-bonds generated for 'chain 'C' and resid 524 through 526' Processing helix chain 'C' and resid 527 through 554 removed outlier: 3.988A pdb=" N MET C 531 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.831A pdb=" N GLN C 569 " --> pdb=" O ASP C 565 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 571 " --> pdb=" O ILE C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 585 removed outlier: 4.571A pdb=" N PHE C 575 " --> pdb=" O THR C 571 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 584 " --> pdb=" O ARG C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 619 removed outlier: 3.514A pdb=" N ASP C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 647 Processing helix chain 'C' and resid 650 through 664 Processing helix chain 'C' and resid 667 through 681 removed outlier: 3.662A pdb=" N ALA C 681 " --> pdb=" O HIS C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 709 removed outlier: 3.619A pdb=" N GLU C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 445 through 455 Processing helix chain 'D' and resid 461 through 488 removed outlier: 3.539A pdb=" N ILE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 501 Processing helix chain 'D' and resid 503 through 524 removed outlier: 3.594A pdb=" N LEU D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 516 " --> pdb=" O ASN D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 555 removed outlier: 3.795A pdb=" N MET D 531 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP D 532 " --> pdb=" O PRO D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 4.208A pdb=" N GLN D 569 " --> pdb=" O ASP D 565 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR D 571 " --> pdb=" O ILE D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 593 through 615 Processing helix chain 'D' and resid 637 through 647 removed outlier: 3.598A pdb=" N HIS D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.934A pdb=" N ARG D 654 " --> pdb=" O ASN D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 682 removed outlier: 3.573A pdb=" N THR D 673 " --> pdb=" O PRO D 669 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 709 removed outlier: 3.713A pdb=" N TYR D 686 " --> pdb=" O GLY D 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 441 Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.759A pdb=" N VAL E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 488 removed outlier: 3.603A pdb=" N ILE E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 503 through 523 removed outlier: 3.809A pdb=" N MET E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU E 520 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 526 No H-bonds generated for 'chain 'E' and resid 524 through 526' Processing helix chain 'E' and resid 527 through 555 removed outlier: 4.057A pdb=" N MET E 531 " --> pdb=" O ASP E 527 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 Processing helix chain 'E' and resid 571 through 586 removed outlier: 4.672A pdb=" N PHE E 575 " --> pdb=" O THR E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 619 removed outlier: 3.646A pdb=" N LEU E 617 " --> pdb=" O ASP E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 647 Processing helix chain 'E' and resid 650 through 664 removed outlier: 3.559A pdb=" N ARG E 654 " --> pdb=" O ASN E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 682 Processing helix chain 'E' and resid 682 through 709 Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.571A pdb=" N LEU F 441 " --> pdb=" O TYR F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 459 removed outlier: 3.559A pdb=" N VAL F 456 " --> pdb=" O ASP F 452 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 487 removed outlier: 3.636A pdb=" N ILE F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 501 Processing helix chain 'F' and resid 503 through 524 removed outlier: 3.771A pdb=" N LEU F 515 " --> pdb=" O ALA F 511 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE F 516 " --> pdb=" O ASN F 512 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 555 removed outlier: 3.944A pdb=" N MET F 531 " --> pdb=" O ASP F 527 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP F 532 " --> pdb=" O PRO F 528 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG F 539 " --> pdb=" O LEU F 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN F 540 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 571 Processing helix chain 'F' and resid 571 through 586 removed outlier: 4.741A pdb=" N PHE F 575 " --> pdb=" O THR F 571 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN F 584 " --> pdb=" O ARG F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 619 Processing helix chain 'F' and resid 637 through 647 Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.604A pdb=" N ARG F 654 " --> pdb=" O ASN F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 681 Processing helix chain 'F' and resid 682 through 708 removed outlier: 3.589A pdb=" N LYS F 690 " --> pdb=" O TYR F 686 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU F 708 " --> pdb=" O SER F 704 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA2, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA3, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'D' and resid 491 through 492 Processing sheet with id=AA5, first strand: chain 'E' and resid 491 through 492 Processing sheet with id=AA6, first strand: chain 'F' and resid 491 through 492 985 hydrogen bonds defined for protein. 2925 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: 3.77 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2670 1.33 - 1.45: 2877 1.45 - 1.57: 7605 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 13290 Sorted by residual: bond pdb=" N VAL F 459 " pdb=" CA VAL F 459 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N VAL A 459 " pdb=" CA VAL A 459 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N PRO A 587 " pdb=" CA PRO A 587 " ideal model delta sigma weight residual 1.465 1.434 0.031 1.10e-02 8.26e+03 8.15e+00 bond pdb=" N LEU F 458 " pdb=" CA LEU F 458 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.35e-02 5.49e+03 7.47e+00 bond pdb=" N LEU A 458 " pdb=" CA LEU A 458 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.27e-02 6.20e+03 7.46e+00 ... (remaining 13285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17487 1.97 - 3.95: 387 3.95 - 5.92: 52 5.92 - 7.90: 10 7.90 - 9.87: 7 Bond angle restraints: 17943 Sorted by residual: angle pdb=" N ASP B 632 " pdb=" CA ASP B 632 " pdb=" C ASP B 632 " ideal model delta sigma weight residual 113.01 105.80 7.21 1.20e+00 6.94e-01 3.61e+01 angle pdb=" N GLU B 633 " pdb=" CA GLU B 633 " pdb=" C GLU B 633 " ideal model delta sigma weight residual 112.41 106.41 6.00 1.30e+00 5.92e-01 2.13e+01 angle pdb=" C PRO B 528 " pdb=" CA PRO B 528 " pdb=" CB PRO B 528 " ideal model delta sigma weight residual 111.85 105.94 5.91 1.42e+00 4.96e-01 1.73e+01 angle pdb=" N MET F 519 " pdb=" CA MET F 519 " pdb=" CB MET F 519 " ideal model delta sigma weight residual 110.16 104.71 5.45 1.48e+00 4.57e-01 1.36e+01 angle pdb=" CA ILE B 533 " pdb=" C ILE B 533 " pdb=" O ILE B 533 " ideal model delta sigma weight residual 121.27 117.56 3.71 1.04e+00 9.25e-01 1.27e+01 ... (remaining 17938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6735 17.96 - 35.92: 974 35.92 - 53.89: 338 53.89 - 71.85: 61 71.85 - 89.81: 35 Dihedral angle restraints: 8143 sinusoidal: 3399 harmonic: 4744 Sorted by residual: dihedral pdb=" CA ASP D 565 " pdb=" CB ASP D 565 " pdb=" CG ASP D 565 " pdb=" OD1 ASP D 565 " ideal model delta sinusoidal sigma weight residual -30.00 -85.61 55.61 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CB GLU C 594 " pdb=" CG GLU C 594 " pdb=" CD GLU C 594 " pdb=" OE1 GLU C 594 " ideal model delta sinusoidal sigma weight residual 0.00 -88.64 88.64 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU E 606 " pdb=" CG GLU E 606 " pdb=" CD GLU E 606 " pdb=" OE1 GLU E 606 " ideal model delta sinusoidal sigma weight residual 0.00 -88.52 88.52 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1821 0.063 - 0.127: 186 0.127 - 0.190: 22 0.190 - 0.253: 0 0.253 - 0.316: 1 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CB VAL F 459 " pdb=" CA VAL F 459 " pdb=" CG1 VAL F 459 " pdb=" CG2 VAL F 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ARG D 492 " pdb=" N ARG D 492 " pdb=" C ARG D 492 " pdb=" CB ARG D 492 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ILE B 533 " pdb=" N ILE B 533 " pdb=" C ILE B 533 " pdb=" CB ILE B 533 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 2027 not shown) Planarity restraints: 2341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 576 " -0.217 9.50e-02 1.11e+02 9.72e-02 5.80e+00 pdb=" NE ARG D 576 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 576 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 576 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 576 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 433 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO B 434 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 464 " 0.191 9.50e-02 1.11e+02 8.58e-02 4.52e+00 pdb=" NE ARG F 464 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 464 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 464 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 464 " 0.007 2.00e-02 2.50e+03 ... (remaining 2338 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2556 2.77 - 3.30: 12591 3.30 - 3.84: 22201 3.84 - 4.37: 25243 4.37 - 4.90: 44351 Nonbonded interactions: 106942 Sorted by model distance: nonbonded pdb=" OD1 ASP E 532 " pdb=" NH2 ARG F 523 " model vdw 2.241 3.120 nonbonded pdb=" OH TYR F 563 " pdb=" OD2 ASP F 613 " model vdw 2.249 3.040 nonbonded pdb=" OE2 GLU A 536 " pdb=" NH1 ARG A 580 " model vdw 2.264 3.120 nonbonded pdb=" OE2 GLU E 560 " pdb=" OH TYR E 638 " model vdw 2.268 3.040 nonbonded pdb=" NH2 ARG E 523 " pdb=" OD1 ASP F 532 " model vdw 2.276 3.120 ... (remaining 106937 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 426 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 709)) selection = (chain 'B' and (resid 426 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 709)) selection = (chain 'C' and (resid 426 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 709)) selection = (chain 'D' and (resid 426 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 709)) selection = chain 'E' selection = (chain 'F' and (resid 426 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 709)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.680 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.004 0.062 13290 Z= 0.233 Angle : 0.688 9.870 17943 Z= 0.416 Chirality : 0.042 0.316 2030 Planarity : 0.006 0.097 2341 Dihedral : 19.523 89.812 5075 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.96 % Favored : 96.36 % Rotamer: Outliers : 4.70 % Allowed : 26.04 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.21), residues: 1622 helix: 2.05 (0.15), residues: 1276 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 457 HIS 0.003 0.001 HIS B 463 PHE 0.015 0.001 PHE E 450 TYR 0.011 0.001 TYR A 686 ARG 0.015 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.15486 ( 985) hydrogen bonds : angle 5.39438 ( 2925) covalent geometry : bond 0.00393 (13290) covalent geometry : angle 0.68797 (17943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 470 time to evaluate : 1.438 Fit side-chains REVERT: A 432 LEU cc_start: 0.7895 (mp) cc_final: 0.7301 (mt) REVERT: A 436 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7278 (mp0) REVERT: A 487 ASP cc_start: 0.7763 (m-30) cc_final: 0.7267 (m-30) REVERT: A 504 THR cc_start: 0.8229 (p) cc_final: 0.7976 (m) REVERT: A 505 GLU cc_start: 0.7941 (mp0) cc_final: 0.7623 (mp0) REVERT: A 520 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7094 (mp0) REVERT: A 645 THR cc_start: 0.8040 (m) cc_final: 0.7678 (p) REVERT: A 661 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7334 (mtm-85) REVERT: A 688 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7741 (mp0) REVERT: B 447 ARG cc_start: 0.8537 (mtt90) cc_final: 0.8306 (mpt180) REVERT: B 448 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: B 470 SER cc_start: 0.8599 (t) cc_final: 0.8283 (p) REVERT: B 505 GLU cc_start: 0.7938 (mp0) cc_final: 0.7727 (mp0) REVERT: B 580 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.8105 (mtp-110) REVERT: B 661 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7646 (ttp-110) REVERT: B 671 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7876 (mttt) REVERT: B 680 GLN cc_start: 0.7778 (mt0) cc_final: 0.7147 (mp10) REVERT: C 436 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7088 (mt-10) REVERT: C 448 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 452 ASP cc_start: 0.7105 (m-30) cc_final: 0.6862 (m-30) REVERT: C 489 SER cc_start: 0.8431 (m) cc_final: 0.8019 (p) REVERT: C 672 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 675 LEU cc_start: 0.8688 (tp) cc_final: 0.8447 (mm) REVERT: C 688 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7838 (mp0) REVERT: D 432 LEU cc_start: 0.8638 (mt) cc_final: 0.8390 (mt) REVERT: D 448 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: D 487 ASP cc_start: 0.7184 (m-30) cc_final: 0.6976 (m-30) REVERT: D 489 SER cc_start: 0.8355 (t) cc_final: 0.7938 (p) REVERT: D 541 LEU cc_start: 0.8425 (tt) cc_final: 0.8187 (mt) REVERT: D 554 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8083 (m110) REVERT: D 556 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7725 (mt-10) REVERT: D 568 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.7180 (mtt-85) REVERT: D 593 LEU cc_start: 0.7681 (pp) cc_final: 0.7465 (pt) REVERT: D 637 SER cc_start: 0.8768 (m) cc_final: 0.8532 (p) REVERT: D 667 ASP cc_start: 0.6949 (p0) cc_final: 0.6552 (p0) REVERT: D 669 PRO cc_start: 0.8892 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: D 671 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8030 (mtmt) REVERT: D 691 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7731 (mtp) REVERT: D 696 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7390 (mp0) REVERT: E 459 VAL cc_start: 0.7919 (m) cc_final: 0.7675 (p) REVERT: E 464 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7653 (mmt90) REVERT: E 470 SER cc_start: 0.8684 (t) cc_final: 0.8418 (p) REVERT: E 483 ASP cc_start: 0.7348 (m-30) cc_final: 0.7043 (m-30) REVERT: E 487 ASP cc_start: 0.7681 (m-30) cc_final: 0.7285 (m-30) REVERT: E 500 MET cc_start: 0.8460 (mmm) cc_final: 0.8190 (mmt) REVERT: E 672 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7188 (mt-10) REVERT: E 680 GLN cc_start: 0.8275 (tp40) cc_final: 0.7816 (tp-100) REVERT: F 460 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7768 (pp) REVERT: F 537 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7373 (tp30) REVERT: F 556 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7547 (mt-10) REVERT: F 581 MET cc_start: 0.8303 (mtt) cc_final: 0.8071 (mtp) REVERT: F 613 ASP cc_start: 0.7680 (m-30) cc_final: 0.7296 (m-30) REVERT: F 633 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5268 (tt0) REVERT: F 661 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7828 (ttm-80) REVERT: F 688 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7534 (mt-10) outliers start: 69 outliers final: 33 residues processed: 512 average time/residue: 1.6388 time to fit residues: 893.6241 Evaluate side-chains 496 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 455 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 673 THR Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 697 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0970 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 GLN A 658 GLN B 512 ASN B 545 GLN C 545 GLN C 609 GLN D 545 GLN E 466 ASN E 545 GLN F 545 GLN F 569 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122769 restraints weight = 16462.118| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.79 r_work: 0.3457 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13290 Z= 0.168 Angle : 0.568 10.612 17943 Z= 0.286 Chirality : 0.038 0.137 2030 Planarity : 0.005 0.047 2341 Dihedral : 7.416 61.057 1871 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.34 % Favored : 97.04 % Rotamer: Outliers : 4.16 % Allowed : 24.34 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.21), residues: 1622 helix: 2.52 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 457 HIS 0.004 0.001 HIS A 430 PHE 0.018 0.001 PHE E 450 TYR 0.018 0.002 TYR F 614 ARG 0.008 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.05485 ( 985) hydrogen bonds : angle 3.82971 ( 2925) covalent geometry : bond 0.00393 (13290) covalent geometry : angle 0.56798 (17943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 480 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8140 (mp) cc_final: 0.7557 (mt) REVERT: A 436 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7205 (mp0) REVERT: A 487 ASP cc_start: 0.7648 (m-30) cc_final: 0.7115 (m-30) REVERT: A 505 GLU cc_start: 0.7956 (mp0) cc_final: 0.7718 (mp0) REVERT: A 520 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7193 (mp0) REVERT: A 521 LYS cc_start: 0.8251 (mttm) cc_final: 0.7977 (mttt) REVERT: A 581 MET cc_start: 0.8332 (mtt) cc_final: 0.8071 (mtt) REVERT: A 645 THR cc_start: 0.8214 (m) cc_final: 0.7890 (p) REVERT: A 672 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7142 (mt-10) REVERT: A 688 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7740 (mp0) REVERT: B 447 ARG cc_start: 0.8402 (mtt90) cc_final: 0.8156 (mpt180) REVERT: B 448 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: B 470 SER cc_start: 0.8610 (t) cc_final: 0.8304 (p) REVERT: B 505 GLU cc_start: 0.7943 (mp0) cc_final: 0.7726 (mp0) REVERT: B 529 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6585 (mtm110) REVERT: B 633 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.5364 (tt0) REVERT: B 661 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7589 (ttm-80) REVERT: B 670 LEU cc_start: 0.8001 (mt) cc_final: 0.7742 (mt) REVERT: C 436 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7071 (mt-10) REVERT: C 448 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: C 452 ASP cc_start: 0.7094 (m-30) cc_final: 0.6874 (m-30) REVERT: C 489 SER cc_start: 0.8525 (m) cc_final: 0.8156 (p) REVERT: C 616 ASN cc_start: 0.8174 (t0) cc_final: 0.7972 (t0) REVERT: C 672 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 676 SER cc_start: 0.8862 (t) cc_final: 0.8499 (m) REVERT: C 704 SER cc_start: 0.8537 (t) cc_final: 0.8173 (p) REVERT: D 432 LEU cc_start: 0.8636 (mt) cc_final: 0.8370 (mt) REVERT: D 487 ASP cc_start: 0.7205 (m-30) cc_final: 0.6911 (m-30) REVERT: D 489 SER cc_start: 0.8382 (t) cc_final: 0.7947 (p) REVERT: D 519 MET cc_start: 0.7262 (tpt) cc_final: 0.6750 (tpt) REVERT: D 541 LEU cc_start: 0.8422 (tt) cc_final: 0.8198 (mt) REVERT: D 556 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 568 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7392 (mtt-85) REVERT: D 637 SER cc_start: 0.8616 (m) cc_final: 0.8393 (t) REVERT: D 667 ASP cc_start: 0.7018 (p0) cc_final: 0.6813 (p0) REVERT: D 671 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7934 (mtmt) REVERT: D 696 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7381 (mt-10) REVERT: E 464 ARG cc_start: 0.8050 (mmt-90) cc_final: 0.7782 (mmt90) REVERT: E 470 SER cc_start: 0.8663 (t) cc_final: 0.8376 (p) REVERT: E 483 ASP cc_start: 0.7376 (m-30) cc_final: 0.7047 (m-30) REVERT: E 487 ASP cc_start: 0.7731 (m-30) cc_final: 0.7299 (m-30) REVERT: E 500 MET cc_start: 0.8513 (mmm) cc_final: 0.8248 (mmt) REVERT: E 512 ASN cc_start: 0.8324 (m-40) cc_final: 0.8116 (m110) REVERT: E 561 GLU cc_start: 0.7399 (mp0) cc_final: 0.7119 (mp0) REVERT: E 672 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7237 (mt-10) REVERT: E 680 GLN cc_start: 0.8319 (tp40) cc_final: 0.7910 (tp-100) REVERT: E 685 GLU cc_start: 0.7740 (mp0) cc_final: 0.7315 (mp0) REVERT: F 460 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8000 (pp) REVERT: F 537 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7498 (tp30) REVERT: F 556 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7526 (mt-10) REVERT: F 576 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.8092 (ttp-110) REVERT: F 581 MET cc_start: 0.8367 (mtt) cc_final: 0.8154 (mtt) REVERT: F 613 ASP cc_start: 0.7759 (m-30) cc_final: 0.7507 (m-30) REVERT: F 633 GLU cc_start: 0.5875 (OUTLIER) cc_final: 0.5512 (tm-30) REVERT: F 693 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7209 (tm-30) outliers start: 61 outliers final: 28 residues processed: 512 average time/residue: 1.5821 time to fit residues: 865.1682 Evaluate side-chains 498 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 464 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 696 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 63 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 106 optimal weight: 0.0870 chunk 93 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 GLN A 658 GLN B 512 ASN B 545 GLN C 466 ASN C 609 GLN D 545 GLN D 647 GLN E 545 GLN F 512 ASN F 545 GLN F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122402 restraints weight = 16450.059| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.79 r_work: 0.3441 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13290 Z= 0.176 Angle : 0.560 9.328 17943 Z= 0.279 Chirality : 0.038 0.121 2030 Planarity : 0.005 0.046 2341 Dihedral : 5.758 59.497 1809 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.71 % Favored : 96.61 % Rotamer: Outliers : 5.04 % Allowed : 24.27 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.21), residues: 1622 helix: 2.57 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -1.96 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 551 HIS 0.004 0.001 HIS E 642 PHE 0.022 0.002 PHE E 450 TYR 0.012 0.002 TYR F 686 ARG 0.010 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.05382 ( 985) hydrogen bonds : angle 3.65761 ( 2925) covalent geometry : bond 0.00417 (13290) covalent geometry : angle 0.55969 (17943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 468 time to evaluate : 1.643 Fit side-chains REVERT: A 432 LEU cc_start: 0.8146 (mp) cc_final: 0.7289 (mt) REVERT: A 436 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7016 (mp0) REVERT: A 487 ASP cc_start: 0.7675 (m-30) cc_final: 0.7155 (m-30) REVERT: A 496 PRO cc_start: 0.8679 (Cg_exo) cc_final: 0.8469 (Cg_endo) REVERT: A 505 GLU cc_start: 0.7982 (mp0) cc_final: 0.7719 (mp0) REVERT: A 520 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7164 (mp0) REVERT: A 521 LYS cc_start: 0.8256 (mttm) cc_final: 0.7915 (mttt) REVERT: A 581 MET cc_start: 0.8376 (mtt) cc_final: 0.8138 (mtt) REVERT: A 645 THR cc_start: 0.8193 (m) cc_final: 0.7858 (p) REVERT: A 670 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7868 (mp) REVERT: A 672 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7156 (mt-10) REVERT: B 447 ARG cc_start: 0.8412 (mtt90) cc_final: 0.8122 (mpt180) REVERT: B 505 GLU cc_start: 0.7939 (mp0) cc_final: 0.7719 (mp0) REVERT: B 537 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7323 (tp30) REVERT: B 633 GLU cc_start: 0.5658 (OUTLIER) cc_final: 0.5382 (tt0) REVERT: B 661 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7657 (ttp-110) REVERT: B 667 ASP cc_start: 0.6518 (p0) cc_final: 0.6168 (p0) REVERT: B 670 LEU cc_start: 0.8045 (mt) cc_final: 0.7791 (mt) REVERT: B 680 GLN cc_start: 0.7744 (mt0) cc_final: 0.7415 (mp10) REVERT: B 688 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7293 (mt-10) REVERT: C 428 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5428 (m-30) REVERT: C 448 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 452 ASP cc_start: 0.7097 (m-30) cc_final: 0.6869 (m-30) REVERT: C 489 SER cc_start: 0.8528 (m) cc_final: 0.8159 (p) REVERT: C 521 LYS cc_start: 0.8329 (mttt) cc_final: 0.8113 (mttt) REVERT: C 616 ASN cc_start: 0.8220 (t0) cc_final: 0.8019 (t0) REVERT: C 672 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 676 SER cc_start: 0.8849 (t) cc_final: 0.8469 (m) REVERT: D 432 LEU cc_start: 0.8625 (mt) cc_final: 0.8263 (mt) REVERT: D 489 SER cc_start: 0.8408 (t) cc_final: 0.7978 (p) REVERT: D 492 ARG cc_start: 0.8265 (tpp-160) cc_final: 0.7861 (ttm-80) REVERT: D 519 MET cc_start: 0.7460 (tpt) cc_final: 0.6932 (tpt) REVERT: D 541 LEU cc_start: 0.8441 (tt) cc_final: 0.8214 (mt) REVERT: D 556 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 568 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7427 (mtt-85) REVERT: D 637 SER cc_start: 0.8715 (m) cc_final: 0.8481 (t) REVERT: D 667 ASP cc_start: 0.7122 (p0) cc_final: 0.6893 (p0) REVERT: D 671 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7884 (mtmt) REVERT: E 464 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7769 (mmt90) REVERT: E 470 SER cc_start: 0.8621 (t) cc_final: 0.8393 (p) REVERT: E 483 ASP cc_start: 0.7405 (m-30) cc_final: 0.7094 (m-30) REVERT: E 487 ASP cc_start: 0.7665 (m-30) cc_final: 0.7260 (m-30) REVERT: E 500 MET cc_start: 0.8499 (mmm) cc_final: 0.8208 (mmt) REVERT: E 505 GLU cc_start: 0.7776 (mp0) cc_final: 0.7454 (mp0) REVERT: E 512 ASN cc_start: 0.8351 (m-40) cc_final: 0.8119 (m110) REVERT: E 561 GLU cc_start: 0.7415 (mp0) cc_final: 0.7168 (mp0) REVERT: E 672 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7188 (mt-10) REVERT: E 680 GLN cc_start: 0.8280 (tp40) cc_final: 0.7959 (tp-100) REVERT: E 685 GLU cc_start: 0.7760 (mp0) cc_final: 0.7325 (mp0) REVERT: F 537 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7494 (tp30) REVERT: F 556 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7551 (mt-10) REVERT: F 581 MET cc_start: 0.8406 (mtt) cc_final: 0.8158 (mtp) REVERT: F 611 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8282 (ttp80) REVERT: F 613 ASP cc_start: 0.7807 (m-30) cc_final: 0.7592 (m-30) REVERT: F 633 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5565 (tt0) REVERT: F 661 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7473 (mtm110) REVERT: F 679 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7978 (ttm110) REVERT: F 688 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7454 (mp0) outliers start: 74 outliers final: 40 residues processed: 513 average time/residue: 1.6666 time to fit residues: 915.6037 Evaluate side-chains 514 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 468 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 696 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN A 473 GLN A 545 GLN B 512 ASN B 545 GLN C 545 GLN C 680 GLN D 545 GLN D 647 GLN E 466 ASN E 545 GLN F 512 ASN F 545 GLN F 569 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122995 restraints weight = 16270.769| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.78 r_work: 0.3452 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13290 Z= 0.145 Angle : 0.528 8.425 17943 Z= 0.264 Chirality : 0.036 0.118 2030 Planarity : 0.005 0.047 2341 Dihedral : 4.892 49.802 1798 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.28 % Favored : 97.04 % Rotamer: Outliers : 4.64 % Allowed : 24.47 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.21), residues: 1622 helix: 2.71 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -1.90 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 457 HIS 0.003 0.001 HIS E 642 PHE 0.022 0.001 PHE E 450 TYR 0.011 0.001 TYR B 614 ARG 0.008 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 985) hydrogen bonds : angle 3.51436 ( 2925) covalent geometry : bond 0.00337 (13290) covalent geometry : angle 0.52809 (17943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 465 time to evaluate : 1.464 Fit side-chains REVERT: A 432 LEU cc_start: 0.8144 (mp) cc_final: 0.7138 (mt) REVERT: A 436 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7029 (mp0) REVERT: A 487 ASP cc_start: 0.7663 (m-30) cc_final: 0.7160 (m-30) REVERT: A 496 PRO cc_start: 0.8691 (Cg_exo) cc_final: 0.8484 (Cg_endo) REVERT: A 505 GLU cc_start: 0.7997 (mp0) cc_final: 0.7747 (mp0) REVERT: A 520 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7204 (mp0) REVERT: A 581 MET cc_start: 0.8369 (mtt) cc_final: 0.8119 (mtt) REVERT: A 613 ASP cc_start: 0.8063 (m-30) cc_final: 0.7857 (m-30) REVERT: A 670 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (mp) REVERT: A 672 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 447 ARG cc_start: 0.8413 (mtt90) cc_final: 0.8146 (mpt180) REVERT: B 448 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: B 505 GLU cc_start: 0.7952 (mp0) cc_final: 0.7736 (mp0) REVERT: B 537 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7266 (tp30) REVERT: B 613 ASP cc_start: 0.8124 (m-30) cc_final: 0.7918 (m-30) REVERT: B 633 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.5304 (tt0) REVERT: B 661 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7659 (ttp-110) REVERT: B 667 ASP cc_start: 0.6511 (p0) cc_final: 0.6157 (p0) REVERT: B 670 LEU cc_start: 0.7976 (mt) cc_final: 0.7749 (mt) REVERT: B 680 GLN cc_start: 0.7764 (mt0) cc_final: 0.7414 (mp10) REVERT: C 448 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: C 452 ASP cc_start: 0.7102 (m-30) cc_final: 0.6876 (m-30) REVERT: C 672 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7558 (mt-10) REVERT: C 676 SER cc_start: 0.8839 (t) cc_final: 0.8441 (m) REVERT: D 432 LEU cc_start: 0.8607 (mt) cc_final: 0.8197 (mt) REVERT: D 489 SER cc_start: 0.8407 (t) cc_final: 0.7956 (p) REVERT: D 492 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.7964 (ttm-80) REVERT: D 541 LEU cc_start: 0.8424 (tt) cc_final: 0.8206 (mt) REVERT: D 548 ASP cc_start: 0.7955 (t70) cc_final: 0.7664 (t0) REVERT: D 556 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7661 (mt-10) REVERT: D 568 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7495 (mtt-85) REVERT: D 611 ARG cc_start: 0.8550 (ttt-90) cc_final: 0.8246 (ttt90) REVERT: D 613 ASP cc_start: 0.7961 (m-30) cc_final: 0.7760 (m-30) REVERT: D 667 ASP cc_start: 0.7126 (p0) cc_final: 0.6869 (p0) REVERT: D 671 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7860 (mtmt) REVERT: E 464 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.7751 (mmt90) REVERT: E 470 SER cc_start: 0.8569 (t) cc_final: 0.8362 (p) REVERT: E 500 MET cc_start: 0.8495 (mmm) cc_final: 0.8236 (mmt) REVERT: E 505 GLU cc_start: 0.7779 (mp0) cc_final: 0.7493 (mp0) REVERT: E 506 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: E 561 GLU cc_start: 0.7445 (mp0) cc_final: 0.7213 (mp0) REVERT: E 672 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7158 (mt-10) REVERT: E 680 GLN cc_start: 0.8291 (tp40) cc_final: 0.7946 (tp-100) REVERT: E 685 GLU cc_start: 0.7782 (mp0) cc_final: 0.7230 (mp0) REVERT: F 537 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7477 (tp30) REVERT: F 556 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7552 (mt-10) REVERT: F 581 MET cc_start: 0.8392 (mtt) cc_final: 0.8136 (mtp) REVERT: F 611 ARG cc_start: 0.8526 (ttp-170) cc_final: 0.8311 (ttp80) REVERT: F 633 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5607 (tt0) REVERT: F 658 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: F 679 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7990 (ttm110) REVERT: F 688 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7413 (mt-10) outliers start: 68 outliers final: 41 residues processed: 506 average time/residue: 1.7138 time to fit residues: 926.0140 Evaluate side-chains 505 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 457 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 696 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 151 optimal weight: 0.1980 chunk 147 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 156 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 545 GLN B 512 ASN B 545 GLN C 545 GLN C 569 GLN C 680 GLN D 455 ASN D 545 GLN D 647 GLN E 466 ASN E 512 ASN E 545 GLN F 512 ASN F 545 GLN F 569 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122601 restraints weight = 16477.248| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.80 r_work: 0.3449 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13290 Z= 0.152 Angle : 0.544 10.177 17943 Z= 0.270 Chirality : 0.037 0.126 2030 Planarity : 0.005 0.047 2341 Dihedral : 4.643 49.645 1796 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.34 % Favored : 97.04 % Rotamer: Outliers : 4.98 % Allowed : 25.09 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.21), residues: 1622 helix: 2.74 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -1.84 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 457 HIS 0.003 0.001 HIS E 642 PHE 0.023 0.001 PHE E 450 TYR 0.012 0.001 TYR B 614 ARG 0.010 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 985) hydrogen bonds : angle 3.47968 ( 2925) covalent geometry : bond 0.00355 (13290) covalent geometry : angle 0.54441 (17943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 465 time to evaluate : 3.222 Fit side-chains REVERT: A 432 LEU cc_start: 0.8161 (mp) cc_final: 0.7188 (mt) REVERT: A 436 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7058 (mp0) REVERT: A 487 ASP cc_start: 0.7682 (m-30) cc_final: 0.7196 (m-30) REVERT: A 505 GLU cc_start: 0.7999 (mp0) cc_final: 0.7734 (mp0) REVERT: A 520 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7158 (mp0) REVERT: A 537 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7608 (mp0) REVERT: A 581 MET cc_start: 0.8397 (mtt) cc_final: 0.8160 (mtt) REVERT: A 613 ASP cc_start: 0.8090 (m-30) cc_final: 0.7859 (m-30) REVERT: A 670 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7842 (mp) REVERT: A 672 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7063 (mt-10) REVERT: B 447 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8123 (mpt180) REVERT: B 448 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: B 505 GLU cc_start: 0.7979 (mp0) cc_final: 0.7763 (mp0) REVERT: B 537 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7290 (tp30) REVERT: B 633 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5306 (tt0) REVERT: B 661 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7695 (ttm-80) REVERT: B 667 ASP cc_start: 0.6508 (p0) cc_final: 0.6127 (p0) REVERT: B 670 LEU cc_start: 0.7983 (mt) cc_final: 0.7764 (mt) REVERT: B 680 GLN cc_start: 0.7764 (mt0) cc_final: 0.7406 (mp10) REVERT: C 448 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: C 452 ASP cc_start: 0.7081 (m-30) cc_final: 0.6852 (m-30) REVERT: C 519 MET cc_start: 0.7989 (mtm) cc_final: 0.7654 (mtm) REVERT: C 672 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7542 (mt-10) REVERT: C 676 SER cc_start: 0.8822 (t) cc_final: 0.8435 (m) REVERT: C 679 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7862 (mtm-85) REVERT: D 428 ASP cc_start: 0.6865 (t0) cc_final: 0.6587 (t0) REVERT: D 432 LEU cc_start: 0.8605 (mt) cc_final: 0.8177 (mt) REVERT: D 487 ASP cc_start: 0.7280 (m-30) cc_final: 0.6980 (m-30) REVERT: D 489 SER cc_start: 0.8409 (t) cc_final: 0.7935 (p) REVERT: D 492 ARG cc_start: 0.8285 (tpp-160) cc_final: 0.7974 (ttm-80) REVERT: D 519 MET cc_start: 0.7518 (tpt) cc_final: 0.7127 (tpt) REVERT: D 541 LEU cc_start: 0.8438 (tt) cc_final: 0.8219 (mt) REVERT: D 548 ASP cc_start: 0.7967 (t70) cc_final: 0.7679 (t0) REVERT: D 556 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7635 (mt-10) REVERT: D 568 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7563 (mtt-85) REVERT: D 611 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8234 (ttt90) REVERT: D 667 ASP cc_start: 0.7181 (p0) cc_final: 0.6932 (p0) REVERT: D 671 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7876 (mtmt) REVERT: E 500 MET cc_start: 0.8507 (mmm) cc_final: 0.8232 (mmt) REVERT: E 505 GLU cc_start: 0.7745 (mp0) cc_final: 0.7471 (mp0) REVERT: E 506 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: E 512 ASN cc_start: 0.8371 (m-40) cc_final: 0.8161 (m110) REVERT: E 561 GLU cc_start: 0.7408 (mp0) cc_final: 0.7175 (mp0) REVERT: E 672 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7134 (mt-10) REVERT: E 680 GLN cc_start: 0.8313 (tp40) cc_final: 0.7960 (tp-100) REVERT: E 685 GLU cc_start: 0.7791 (mp0) cc_final: 0.7247 (mp0) REVERT: F 537 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7397 (tp30) REVERT: F 556 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7544 (mt-10) REVERT: F 581 MET cc_start: 0.8407 (mtt) cc_final: 0.8150 (mtp) REVERT: F 583 VAL cc_start: 0.8098 (t) cc_final: 0.7838 (m) REVERT: F 611 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.8358 (ttp80) REVERT: F 633 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5578 (tt0) REVERT: F 658 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: F 688 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7353 (mt-10) outliers start: 73 outliers final: 48 residues processed: 510 average time/residue: 1.9004 time to fit residues: 1037.2513 Evaluate side-chains 525 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 468 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 679 ARG Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 696 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 545 GLN B 512 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN C 680 GLN D 545 GLN D 647 GLN E 466 ASN F 512 ASN F 545 GLN F 569 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121166 restraints weight = 16675.720| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.80 r_work: 0.3433 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13290 Z= 0.212 Angle : 0.592 10.065 17943 Z= 0.294 Chirality : 0.040 0.127 2030 Planarity : 0.005 0.051 2341 Dihedral : 4.661 47.011 1794 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.40 % Favored : 96.92 % Rotamer: Outliers : 4.98 % Allowed : 25.63 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.21), residues: 1622 helix: 2.56 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -1.83 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 551 HIS 0.004 0.001 HIS B 463 PHE 0.023 0.002 PHE E 450 TYR 0.016 0.002 TYR A 614 ARG 0.010 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.05549 ( 985) hydrogen bonds : angle 3.58461 ( 2925) covalent geometry : bond 0.00512 (13290) covalent geometry : angle 0.59247 (17943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 472 time to evaluate : 1.477 Fit side-chains REVERT: A 432 LEU cc_start: 0.8275 (mp) cc_final: 0.7660 (mt) REVERT: A 436 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7156 (mp0) REVERT: A 487 ASP cc_start: 0.7710 (m-30) cc_final: 0.7239 (m-30) REVERT: A 505 GLU cc_start: 0.8008 (mp0) cc_final: 0.7750 (mp0) REVERT: A 520 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7131 (mp0) REVERT: A 521 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8045 (mtpt) REVERT: A 581 MET cc_start: 0.8440 (mtt) cc_final: 0.8181 (mtt) REVERT: A 613 ASP cc_start: 0.8100 (m-30) cc_final: 0.7861 (m-30) REVERT: A 670 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7853 (mp) REVERT: A 672 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7078 (mt-10) REVERT: B 447 ARG cc_start: 0.8418 (mtt90) cc_final: 0.8158 (mpt180) REVERT: B 448 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: B 505 GLU cc_start: 0.7975 (mp0) cc_final: 0.7748 (mp0) REVERT: B 537 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7326 (tp30) REVERT: B 633 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.5419 (tt0) REVERT: B 658 GLN cc_start: 0.8144 (tp40) cc_final: 0.7925 (tp40) REVERT: B 661 ARG cc_start: 0.7981 (tpp80) cc_final: 0.7707 (ttm-80) REVERT: B 667 ASP cc_start: 0.6578 (p0) cc_final: 0.6202 (p0) REVERT: B 670 LEU cc_start: 0.8040 (mt) cc_final: 0.7819 (mt) REVERT: B 680 GLN cc_start: 0.7811 (mt0) cc_final: 0.7444 (mp10) REVERT: C 448 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: C 452 ASP cc_start: 0.7085 (m-30) cc_final: 0.6852 (m-30) REVERT: C 672 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7567 (mt-10) REVERT: C 676 SER cc_start: 0.8833 (t) cc_final: 0.8461 (m) REVERT: C 679 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7729 (mpp80) REVERT: C 696 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: D 487 ASP cc_start: 0.7322 (m-30) cc_final: 0.7031 (m-30) REVERT: D 541 LEU cc_start: 0.8463 (tt) cc_final: 0.8251 (mt) REVERT: D 548 ASP cc_start: 0.7979 (t70) cc_final: 0.7690 (t0) REVERT: D 556 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 568 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7489 (mtt-85) REVERT: D 667 ASP cc_start: 0.7193 (p0) cc_final: 0.6960 (p0) REVERT: D 671 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7894 (mtmt) REVERT: E 500 MET cc_start: 0.8517 (mmm) cc_final: 0.8252 (mmt) REVERT: E 505 GLU cc_start: 0.7790 (mp0) cc_final: 0.7508 (mp0) REVERT: E 506 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: E 561 GLU cc_start: 0.7441 (mp0) cc_final: 0.7238 (mp0) REVERT: E 672 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7171 (mt-10) REVERT: E 680 GLN cc_start: 0.8311 (tp40) cc_final: 0.7950 (tp-100) REVERT: E 685 GLU cc_start: 0.7781 (mp0) cc_final: 0.7279 (mp0) REVERT: F 537 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7506 (tp30) REVERT: F 556 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7547 (mt-10) REVERT: F 580 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8071 (mtp180) REVERT: F 581 MET cc_start: 0.8415 (mtt) cc_final: 0.8162 (mtp) REVERT: F 583 VAL cc_start: 0.8067 (t) cc_final: 0.7788 (m) REVERT: F 658 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: F 688 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7377 (mt-10) outliers start: 73 outliers final: 48 residues processed: 512 average time/residue: 1.5775 time to fit residues: 863.5155 Evaluate side-chains 522 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 464 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 679 ARG Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 90 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 140 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 50 optimal weight: 0.0570 chunk 29 optimal weight: 0.6980 chunk 160 optimal weight: 0.2980 chunk 147 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 545 GLN B 512 ASN C 545 GLN C 680 GLN D 545 GLN D 647 GLN E 466 ASN E 512 ASN F 512 ASN F 524 GLN F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123453 restraints weight = 16394.441| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.80 r_work: 0.3466 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13290 Z= 0.132 Angle : 0.552 9.846 17943 Z= 0.276 Chirality : 0.036 0.114 2030 Planarity : 0.005 0.051 2341 Dihedral : 4.291 45.303 1791 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.22 % Favored : 97.16 % Rotamer: Outliers : 4.64 % Allowed : 26.58 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.21), residues: 1622 helix: 2.76 (0.14), residues: 1301 sheet: None (None), residues: 0 loop : -1.71 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 551 HIS 0.003 0.001 HIS B 430 PHE 0.022 0.001 PHE E 450 TYR 0.012 0.001 TYR A 614 ARG 0.012 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 985) hydrogen bonds : angle 3.45176 ( 2925) covalent geometry : bond 0.00298 (13290) covalent geometry : angle 0.55184 (17943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 472 time to evaluate : 1.998 Fit side-chains REVERT: A 432 LEU cc_start: 0.8163 (mp) cc_final: 0.7069 (mt) REVERT: A 436 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7027 (mp0) REVERT: A 487 ASP cc_start: 0.7676 (m-30) cc_final: 0.7233 (m-30) REVERT: A 505 GLU cc_start: 0.7981 (mp0) cc_final: 0.7712 (mp0) REVERT: A 520 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7193 (mp0) REVERT: A 521 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7985 (mtpt) REVERT: A 537 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7711 (mp0) REVERT: A 670 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 672 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7062 (mt-10) REVERT: B 447 ARG cc_start: 0.8386 (mtt90) cc_final: 0.8110 (mpt180) REVERT: B 448 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: B 505 GLU cc_start: 0.7948 (mp0) cc_final: 0.7730 (mp0) REVERT: B 537 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7269 (tp30) REVERT: B 633 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5424 (tt0) REVERT: B 661 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7681 (ttm-80) REVERT: B 667 ASP cc_start: 0.6558 (p0) cc_final: 0.6188 (p0) REVERT: B 680 GLN cc_start: 0.7746 (mt0) cc_final: 0.7359 (mp10) REVERT: B 688 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7194 (mp0) REVERT: C 448 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: C 452 ASP cc_start: 0.7080 (m-30) cc_final: 0.6836 (m-30) REVERT: C 672 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 676 SER cc_start: 0.8823 (t) cc_final: 0.8421 (m) REVERT: C 680 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7383 (tm130) REVERT: C 696 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: D 432 LEU cc_start: 0.8573 (mt) cc_final: 0.8223 (mt) REVERT: D 487 ASP cc_start: 0.7309 (m-30) cc_final: 0.6996 (m-30) REVERT: D 489 SER cc_start: 0.8407 (t) cc_final: 0.8021 (p) REVERT: D 492 ARG cc_start: 0.8286 (tpp-160) cc_final: 0.7981 (ttm-80) REVERT: D 541 LEU cc_start: 0.8421 (tt) cc_final: 0.8200 (mt) REVERT: D 548 ASP cc_start: 0.7957 (t70) cc_final: 0.7668 (t0) REVERT: D 556 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 568 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7529 (mtt-85) REVERT: D 611 ARG cc_start: 0.8533 (ttt-90) cc_final: 0.8227 (ttt90) REVERT: D 667 ASP cc_start: 0.7163 (p0) cc_final: 0.6932 (p0) REVERT: D 671 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7850 (mtmt) REVERT: E 500 MET cc_start: 0.8504 (mmm) cc_final: 0.8266 (mmt) REVERT: E 505 GLU cc_start: 0.7708 (mp0) cc_final: 0.7460 (mp0) REVERT: E 512 ASN cc_start: 0.8362 (m-40) cc_final: 0.8127 (m110) REVERT: E 561 GLU cc_start: 0.7414 (mp0) cc_final: 0.7203 (mp0) REVERT: E 672 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7107 (mt-10) REVERT: E 680 GLN cc_start: 0.8308 (tp40) cc_final: 0.7955 (tp-100) REVERT: E 685 GLU cc_start: 0.7770 (mp0) cc_final: 0.7197 (mp0) REVERT: F 537 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7465 (tp30) REVERT: F 556 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7551 (mt-10) REVERT: F 581 MET cc_start: 0.8390 (mtt) cc_final: 0.8135 (mtp) REVERT: F 583 VAL cc_start: 0.8092 (t) cc_final: 0.7826 (m) REVERT: F 611 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.8347 (ttp80) REVERT: F 617 LEU cc_start: 0.8558 (tp) cc_final: 0.8325 (mt) REVERT: F 658 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: F 679 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7955 (ttm170) REVERT: F 688 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7294 (mt-10) outliers start: 68 outliers final: 44 residues processed: 510 average time/residue: 1.6362 time to fit residues: 893.7784 Evaluate side-chains 525 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 473 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 671 LYS Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.6980 chunk 151 optimal weight: 0.0980 chunk 6 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 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 473 GLN A 545 GLN B 512 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN D 545 GLN D 647 GLN E 466 ASN E 596 GLN F 545 GLN F 569 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122435 restraints weight = 16522.881| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.80 r_work: 0.3448 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13290 Z= 0.167 Angle : 0.588 11.778 17943 Z= 0.293 Chirality : 0.038 0.128 2030 Planarity : 0.005 0.048 2341 Dihedral : 4.271 45.841 1790 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.22 % Favored : 97.16 % Rotamer: Outliers : 4.77 % Allowed : 27.81 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.21), residues: 1622 helix: 2.67 (0.14), residues: 1297 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 551 HIS 0.003 0.001 HIS B 463 PHE 0.024 0.002 PHE E 450 TYR 0.019 0.002 TYR A 614 ARG 0.011 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.05006 ( 985) hydrogen bonds : angle 3.51573 ( 2925) covalent geometry : bond 0.00399 (13290) covalent geometry : angle 0.58836 (17943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 458 time to evaluate : 1.499 Fit side-chains REVERT: A 432 LEU cc_start: 0.8211 (mp) cc_final: 0.7256 (mt) REVERT: A 436 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7074 (mp0) REVERT: A 487 ASP cc_start: 0.7667 (m-30) cc_final: 0.7231 (m-30) REVERT: A 505 GLU cc_start: 0.8000 (mp0) cc_final: 0.7727 (mp0) REVERT: A 520 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7222 (mp0) REVERT: A 521 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8039 (mtpt) REVERT: A 611 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8129 (ttt-90) REVERT: A 613 ASP cc_start: 0.8037 (m-30) cc_final: 0.7802 (m-30) REVERT: A 670 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 672 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7045 (mt-10) REVERT: B 447 ARG cc_start: 0.8400 (mtt90) cc_final: 0.8125 (mpt180) REVERT: B 448 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: B 505 GLU cc_start: 0.7958 (mp0) cc_final: 0.7749 (mp0) REVERT: B 537 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7279 (tp30) REVERT: B 633 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5513 (tt0) REVERT: B 637 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 661 ARG cc_start: 0.7981 (tpp80) cc_final: 0.7683 (ttm-80) REVERT: B 680 GLN cc_start: 0.7783 (mt0) cc_final: 0.7402 (mp10) REVERT: C 448 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: C 452 ASP cc_start: 0.7074 (m-30) cc_final: 0.6839 (m-30) REVERT: C 672 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7552 (mt-10) REVERT: C 676 SER cc_start: 0.8819 (t) cc_final: 0.8425 (m) REVERT: C 680 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7420 (tm130) REVERT: C 696 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: D 432 LEU cc_start: 0.8588 (mt) cc_final: 0.8186 (mt) REVERT: D 487 ASP cc_start: 0.7347 (m-30) cc_final: 0.7032 (m-30) REVERT: D 519 MET cc_start: 0.7338 (tpt) cc_final: 0.7086 (tpt) REVERT: D 541 LEU cc_start: 0.8448 (tt) cc_final: 0.8224 (mt) REVERT: D 548 ASP cc_start: 0.7960 (t70) cc_final: 0.7680 (t0) REVERT: D 556 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 568 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7525 (mtt-85) REVERT: D 667 ASP cc_start: 0.7173 (p0) cc_final: 0.6941 (p0) REVERT: D 671 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7880 (mtmt) REVERT: E 500 MET cc_start: 0.8502 (mmm) cc_final: 0.8260 (mmt) REVERT: E 505 GLU cc_start: 0.7734 (mp0) cc_final: 0.7453 (mp0) REVERT: E 506 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: E 537 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7948 (mp0) REVERT: E 561 GLU cc_start: 0.7436 (mp0) cc_final: 0.7230 (mp0) REVERT: E 672 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7148 (mt-10) REVERT: E 680 GLN cc_start: 0.8306 (tp40) cc_final: 0.7957 (tp-100) REVERT: E 685 GLU cc_start: 0.7774 (mp0) cc_final: 0.7241 (mp0) REVERT: E 704 SER cc_start: 0.7982 (t) cc_final: 0.7629 (p) REVERT: F 537 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7388 (tp30) REVERT: F 556 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7570 (mt-10) REVERT: F 581 MET cc_start: 0.8399 (mtt) cc_final: 0.8154 (mtp) REVERT: F 583 VAL cc_start: 0.8060 (t) cc_final: 0.7788 (m) REVERT: F 611 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8352 (ttp80) REVERT: F 658 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: F 679 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7954 (ttm170) REVERT: F 688 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7298 (mt-10) outliers start: 70 outliers final: 48 residues processed: 499 average time/residue: 1.5772 time to fit residues: 842.4320 Evaluate side-chains 511 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 453 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 127 optimal weight: 0.0970 chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 545 GLN B 512 ASN C 545 GLN D 545 GLN D 647 GLN E 466 ASN E 596 GLN F 569 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123080 restraints weight = 16576.322| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.81 r_work: 0.3453 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13290 Z= 0.145 Angle : 0.594 15.487 17943 Z= 0.295 Chirality : 0.037 0.131 2030 Planarity : 0.005 0.058 2341 Dihedral : 4.233 45.237 1790 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.03 % Favored : 97.29 % Rotamer: Outliers : 4.36 % Allowed : 27.95 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.21), residues: 1622 helix: 2.72 (0.14), residues: 1298 sheet: None (None), residues: 0 loop : -1.68 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 457 HIS 0.003 0.001 HIS B 430 PHE 0.025 0.001 PHE E 450 TYR 0.018 0.002 TYR A 614 ARG 0.014 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 985) hydrogen bonds : angle 3.48972 ( 2925) covalent geometry : bond 0.00337 (13290) covalent geometry : angle 0.59369 (17943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 468 time to evaluate : 1.986 Fit side-chains REVERT: A 432 LEU cc_start: 0.8166 (mp) cc_final: 0.7176 (mt) REVERT: A 436 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7080 (mp0) REVERT: A 487 ASP cc_start: 0.7642 (m-30) cc_final: 0.7201 (m-30) REVERT: A 492 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7636 (ttm110) REVERT: A 505 GLU cc_start: 0.7971 (mp0) cc_final: 0.7700 (mp0) REVERT: A 521 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8014 (mtpt) REVERT: A 523 ARG cc_start: 0.8371 (mtp85) cc_final: 0.8148 (mmm160) REVERT: A 537 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7598 (mp0) REVERT: A 670 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7810 (mp) REVERT: A 672 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7056 (mt-10) REVERT: B 447 ARG cc_start: 0.8397 (mtt90) cc_final: 0.8117 (mpt180) REVERT: B 448 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: B 505 GLU cc_start: 0.7980 (mp0) cc_final: 0.7768 (mp0) REVERT: B 537 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7314 (tp30) REVERT: B 633 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5502 (tt0) REVERT: B 637 SER cc_start: 0.8735 (m) cc_final: 0.8514 (p) REVERT: B 661 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7643 (ttm-80) REVERT: B 680 GLN cc_start: 0.7771 (mt0) cc_final: 0.7386 (mp10) REVERT: C 448 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: C 452 ASP cc_start: 0.7094 (m-30) cc_final: 0.6852 (m-30) REVERT: C 672 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7557 (mt-10) REVERT: C 676 SER cc_start: 0.8825 (t) cc_final: 0.8426 (m) REVERT: C 680 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7480 (tm130) REVERT: C 696 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: D 432 LEU cc_start: 0.8563 (mt) cc_final: 0.8177 (mt) REVERT: D 487 ASP cc_start: 0.7316 (m-30) cc_final: 0.7007 (m-30) REVERT: D 489 SER cc_start: 0.8453 (t) cc_final: 0.8091 (p) REVERT: D 519 MET cc_start: 0.7303 (tpt) cc_final: 0.7072 (tpt) REVERT: D 541 LEU cc_start: 0.8431 (tt) cc_final: 0.8210 (mt) REVERT: D 556 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7620 (mt-10) REVERT: D 565 ASP cc_start: 0.7565 (m-30) cc_final: 0.7321 (m-30) REVERT: D 568 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7587 (mtt-85) REVERT: D 667 ASP cc_start: 0.7169 (p0) cc_final: 0.6937 (p0) REVERT: D 671 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7879 (mtmt) REVERT: E 500 MET cc_start: 0.8513 (mmm) cc_final: 0.8238 (mmt) REVERT: E 505 GLU cc_start: 0.7750 (mp0) cc_final: 0.7497 (mp0) REVERT: E 506 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: E 672 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7117 (mt-10) REVERT: E 680 GLN cc_start: 0.8335 (tp40) cc_final: 0.7976 (tp-100) REVERT: E 704 SER cc_start: 0.7971 (t) cc_final: 0.7611 (p) REVERT: F 537 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7391 (tp30) REVERT: F 556 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7561 (mt-10) REVERT: F 581 MET cc_start: 0.8406 (mtt) cc_final: 0.8171 (mtt) REVERT: F 583 VAL cc_start: 0.8085 (t) cc_final: 0.7812 (m) REVERT: F 611 ARG cc_start: 0.8565 (ttp-170) cc_final: 0.8359 (ttp80) REVERT: F 617 LEU cc_start: 0.8544 (tp) cc_final: 0.8294 (mt) REVERT: F 658 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8098 (tp40) REVERT: F 661 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7577 (ttm110) REVERT: F 679 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7896 (ttm170) REVERT: F 688 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7290 (mt-10) outliers start: 64 outliers final: 45 residues processed: 507 average time/residue: 1.8106 time to fit residues: 983.5641 Evaluate side-chains 509 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 455 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 134 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 21 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 545 GLN B 512 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN D 647 GLN E 466 ASN E 512 ASN E 596 GLN F 512 ASN F 545 GLN F 569 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122389 restraints weight = 16477.275| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.79 r_work: 0.3445 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13290 Z= 0.167 Angle : 0.624 20.793 17943 Z= 0.308 Chirality : 0.039 0.148 2030 Planarity : 0.005 0.055 2341 Dihedral : 4.136 45.663 1788 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.16 % Favored : 97.16 % Rotamer: Outliers : 4.50 % Allowed : 28.43 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.21), residues: 1622 helix: 2.66 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -1.67 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 457 HIS 0.003 0.001 HIS B 430 PHE 0.025 0.002 PHE E 450 TYR 0.022 0.002 TYR A 614 ARG 0.014 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 985) hydrogen bonds : angle 3.54547 ( 2925) covalent geometry : bond 0.00396 (13290) covalent geometry : angle 0.62442 (17943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 458 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8196 (mp) cc_final: 0.7274 (mt) REVERT: A 436 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7113 (mp0) REVERT: A 487 ASP cc_start: 0.7659 (m-30) cc_final: 0.7228 (m-30) REVERT: A 505 GLU cc_start: 0.7935 (mp0) cc_final: 0.7666 (mp0) REVERT: A 521 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8062 (mtpt) REVERT: A 537 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7673 (mp0) REVERT: A 670 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 672 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7036 (mt-10) REVERT: B 448 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: B 505 GLU cc_start: 0.7969 (mp0) cc_final: 0.7750 (mp0) REVERT: B 537 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7322 (tp30) REVERT: B 633 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5530 (tt0) REVERT: B 637 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 661 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7624 (ttm170) REVERT: B 680 GLN cc_start: 0.7789 (mt0) cc_final: 0.7404 (mp10) REVERT: B 688 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7246 (mp0) REVERT: C 448 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: C 452 ASP cc_start: 0.7083 (m-30) cc_final: 0.6845 (m-30) REVERT: C 672 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 676 SER cc_start: 0.8830 (t) cc_final: 0.8430 (m) REVERT: C 680 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7584 (tm130) REVERT: C 696 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: D 432 LEU cc_start: 0.8573 (mt) cc_final: 0.8219 (mt) REVERT: D 487 ASP cc_start: 0.7322 (m-30) cc_final: 0.7017 (m-30) REVERT: D 489 SER cc_start: 0.8465 (t) cc_final: 0.8098 (p) REVERT: D 492 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.7996 (ttm-80) REVERT: D 541 LEU cc_start: 0.8450 (tt) cc_final: 0.8222 (mt) REVERT: D 556 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7611 (mt-10) REVERT: D 565 ASP cc_start: 0.7573 (m-30) cc_final: 0.7349 (m-30) REVERT: D 568 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7582 (mtt-85) REVERT: D 658 GLN cc_start: 0.8317 (tp-100) cc_final: 0.8068 (mm-40) REVERT: D 667 ASP cc_start: 0.7170 (p0) cc_final: 0.6931 (p0) REVERT: D 671 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7871 (mtmt) REVERT: E 487 ASP cc_start: 0.7696 (m-30) cc_final: 0.7326 (m-30) REVERT: E 500 MET cc_start: 0.8518 (mmm) cc_final: 0.8305 (mmt) REVERT: E 505 GLU cc_start: 0.7760 (mp0) cc_final: 0.7497 (mp0) REVERT: E 506 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: E 672 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7100 (mt-10) REVERT: E 680 GLN cc_start: 0.8313 (tp40) cc_final: 0.7951 (tp-100) REVERT: E 704 SER cc_start: 0.7967 (t) cc_final: 0.7625 (p) REVERT: F 537 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7412 (tp30) REVERT: F 556 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7549 (mt-10) REVERT: F 581 MET cc_start: 0.8405 (mtt) cc_final: 0.8158 (mtp) REVERT: F 583 VAL cc_start: 0.8061 (t) cc_final: 0.7794 (m) REVERT: F 611 ARG cc_start: 0.8557 (ttp-170) cc_final: 0.8354 (ttp80) REVERT: F 617 LEU cc_start: 0.8544 (tp) cc_final: 0.8308 (mt) REVERT: F 658 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: F 688 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7276 (mt-10) outliers start: 66 outliers final: 50 residues processed: 496 average time/residue: 1.5512 time to fit residues: 822.9106 Evaluate side-chains 527 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 467 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 529 ARG Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 527 ASP Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 0.3980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 545 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 545 GLN D 545 GLN D 647 GLN E 466 ASN E 512 ASN E 596 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123294 restraints weight = 16472.978| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.79 r_work: 0.3459 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13290 Z= 0.149 Angle : 0.640 22.608 17943 Z= 0.313 Chirality : 0.038 0.170 2030 Planarity : 0.005 0.058 2341 Dihedral : 4.136 45.169 1788 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.74 % Allowed : 2.10 % Favored : 97.16 % Rotamer: Outliers : 4.50 % Allowed : 28.36 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1622 helix: 2.67 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.60 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 457 HIS 0.003 0.001 HIS B 430 PHE 0.025 0.001 PHE E 450 TYR 0.023 0.002 TYR A 614 ARG 0.013 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 985) hydrogen bonds : angle 3.52858 ( 2925) covalent geometry : bond 0.00348 (13290) covalent geometry : angle 0.63965 (17943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15565.72 seconds wall clock time: 271 minutes 36.70 seconds (16296.70 seconds total)