Starting phenix.real_space_refine on Thu Sep 18 01:42:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2h_47452/09_2025/9e2h_47452.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2h_47452/09_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_47452/09_2025/9e2h_47452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2h_47452/09_2025/9e2h_47452.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2h_47452/09_2025/9e2h_47452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2h_47452/09_2025/9e2h_47452.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.99, per 1000 atoms: 0.31 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: 1.23 Conformation dependent library (CDL) restraints added in 700.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.43 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: 2.23 Time building geometry restraints manager: 1.70 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: 6.470 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.720 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG F 661 TYR 0.011 0.001 TYR A 686 PHE 0.015 0.001 PHE E 450 TRP 0.007 0.001 TRP C 457 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00393 (13290) covalent geometry : angle 0.68797 (17943) hydrogen bonds : bond 0.15486 ( 985) hydrogen bonds : angle 5.39438 ( 2925) *********************** 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 : 0.544 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: 0.8012 time to fit residues: 436.5658 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 : 0.499 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.135224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122813 restraints weight = 16430.923| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.79 r_work: 0.3453 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0990 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 : 0.569 10.762 17943 Z= 0.286 Chirality : 0.038 0.131 2030 Planarity : 0.005 0.046 2341 Dihedral : 7.419 61.331 1871 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.21), residues: 1622 helix: 2.53 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 661 TYR 0.018 0.002 TYR F 614 PHE 0.018 0.001 PHE E 450 TRP 0.003 0.001 TRP C 457 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00393 (13290) covalent geometry : angle 0.56882 (17943) hydrogen bonds : bond 0.05456 ( 985) hydrogen bonds : angle 3.83367 ( 2925) *********************** 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 : 0.462 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8134 (mp) cc_final: 0.7552 (mt) REVERT: A 436 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7211 (mp0) REVERT: A 487 ASP cc_start: 0.7647 (m-30) cc_final: 0.7113 (m-30) REVERT: A 505 GLU cc_start: 0.7955 (mp0) cc_final: 0.7720 (mp0) REVERT: A 520 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7194 (mp0) REVERT: A 521 LYS cc_start: 0.8247 (mttm) cc_final: 0.7978 (mttt) REVERT: A 645 THR cc_start: 0.8212 (m) cc_final: 0.7888 (p) REVERT: A 658 GLN cc_start: 0.7990 (tp40) cc_final: 0.7784 (tp-100) REVERT: A 672 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 688 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7775 (mp0) REVERT: B 447 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8150 (mpt180) REVERT: B 448 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: B 470 SER cc_start: 0.8614 (t) cc_final: 0.8306 (p) REVERT: B 505 GLU cc_start: 0.7942 (mp0) cc_final: 0.7725 (mp0) REVERT: B 529 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6601 (mtm110) REVERT: B 633 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.5367 (tt0) REVERT: B 661 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7588 (ttm-80) REVERT: B 670 LEU cc_start: 0.8003 (mt) cc_final: 0.7747 (mt) REVERT: C 436 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7049 (mt-10) REVERT: C 448 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: C 452 ASP cc_start: 0.7096 (m-30) cc_final: 0.6877 (m-30) REVERT: C 489 SER cc_start: 0.8526 (m) cc_final: 0.8155 (p) REVERT: C 616 ASN cc_start: 0.8174 (t0) cc_final: 0.7971 (t0) REVERT: C 672 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 676 SER cc_start: 0.8860 (t) cc_final: 0.8491 (m) REVERT: C 704 SER cc_start: 0.8535 (t) cc_final: 0.8172 (p) REVERT: D 432 LEU cc_start: 0.8636 (mt) cc_final: 0.8372 (mt) REVERT: D 487 ASP cc_start: 0.7202 (m-30) cc_final: 0.6908 (m-30) REVERT: D 489 SER cc_start: 0.8382 (t) cc_final: 0.7945 (p) REVERT: D 519 MET cc_start: 0.7256 (tpt) cc_final: 0.6730 (tpt) REVERT: D 541 LEU cc_start: 0.8419 (tt) cc_final: 0.8195 (mt) REVERT: D 556 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7733 (mt-10) REVERT: D 568 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7401 (mtt-85) REVERT: D 637 SER cc_start: 0.8622 (m) cc_final: 0.8395 (t) REVERT: D 667 ASP cc_start: 0.7020 (p0) cc_final: 0.6811 (p0) REVERT: D 671 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7942 (mtmt) REVERT: E 464 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7781 (mmt90) REVERT: E 470 SER cc_start: 0.8665 (t) cc_final: 0.8378 (p) REVERT: E 483 ASP cc_start: 0.7372 (m-30) cc_final: 0.7042 (m-30) REVERT: E 487 ASP cc_start: 0.7730 (m-30) cc_final: 0.7296 (m-30) REVERT: E 500 MET cc_start: 0.8510 (mmm) cc_final: 0.8241 (mmt) REVERT: E 512 ASN cc_start: 0.8320 (m-40) cc_final: 0.8112 (m110) REVERT: E 532 ASP cc_start: 0.7480 (m-30) cc_final: 0.7254 (m-30) REVERT: E 561 GLU cc_start: 0.7400 (mp0) cc_final: 0.7117 (mp0) REVERT: E 672 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7237 (mt-10) REVERT: E 680 GLN cc_start: 0.8315 (tp40) cc_final: 0.7905 (tp-100) REVERT: E 685 GLU cc_start: 0.7745 (mp0) cc_final: 0.7319 (mp0) REVERT: F 460 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7991 (pp) REVERT: F 523 ARG cc_start: 0.8510 (mtm180) cc_final: 0.8252 (mtm180) REVERT: F 537 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7501 (tp30) REVERT: F 556 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7529 (mt-10) REVERT: F 576 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.8071 (ttp-110) REVERT: F 580 ARG cc_start: 0.8349 (mtp180) cc_final: 0.8129 (mtp180) REVERT: F 581 MET cc_start: 0.8370 (mtt) cc_final: 0.8160 (mtt) REVERT: F 613 ASP cc_start: 0.7753 (m-30) cc_final: 0.7519 (m-30) REVERT: F 633 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5505 (tm-30) REVERT: F 693 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7212 (tm-30) outliers start: 61 outliers final: 29 residues processed: 513 average time/residue: 0.7908 time to fit residues: 432.0762 Evaluate side-chains 501 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 466 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 489 SER 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 106 optimal weight: 0.2980 chunk 10 optimal weight: 0.0010 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 GLN B 512 ASN B 545 GLN C 466 ASN C 609 GLN D 545 GLN E 545 GLN F 512 ASN 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 = 0.3755 r_free = 0.3755 target = 0.135967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123443 restraints weight = 16577.520| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.82 r_work: 0.3462 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1291 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= 0.141 Angle : 0.537 9.503 17943 Z= 0.268 Chirality : 0.036 0.114 2030 Planarity : 0.005 0.044 2341 Dihedral : 5.674 59.048 1809 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.40 % Favored : 96.98 % Rotamer: Outliers : 4.43 % Allowed : 24.81 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.21), residues: 1622 helix: 2.68 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -1.94 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 539 TYR 0.010 0.001 TYR F 686 PHE 0.021 0.001 PHE E 450 TRP 0.002 0.001 TRP B 457 HIS 0.003 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00324 (13290) covalent geometry : angle 0.53704 (17943) hydrogen bonds : bond 0.04891 ( 985) hydrogen bonds : angle 3.58194 ( 2925) *********************** 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 533 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 468 time to evaluate : 0.527 Fit side-chains REVERT: A 432 LEU cc_start: 0.8144 (mp) cc_final: 0.7155 (mt) REVERT: A 436 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6968 (mp0) REVERT: A 487 ASP cc_start: 0.7655 (m-30) cc_final: 0.7132 (m-30) REVERT: A 496 PRO cc_start: 0.8692 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: A 505 GLU cc_start: 0.7954 (mp0) cc_final: 0.7695 (mp0) REVERT: A 520 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7138 (mp0) REVERT: A 521 LYS cc_start: 0.8246 (mttm) cc_final: 0.7912 (mttt) REVERT: A 581 MET cc_start: 0.8339 (mtt) cc_final: 0.8053 (mtt) REVERT: A 645 THR cc_start: 0.8188 (m) cc_final: 0.7856 (p) REVERT: A 670 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 672 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 684 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7588 (mm) REVERT: B 447 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8168 (mpt180) REVERT: B 505 GLU cc_start: 0.7932 (mp0) cc_final: 0.7706 (mp0) REVERT: B 537 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7290 (tp30) REVERT: B 539 ARG cc_start: 0.8275 (ttt90) cc_final: 0.8024 (ttt-90) REVERT: B 633 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5387 (tt0) REVERT: B 661 ARG cc_start: 0.7947 (tpp80) cc_final: 0.7666 (ttp-110) REVERT: B 667 ASP cc_start: 0.6483 (p0) cc_final: 0.6137 (p0) REVERT: B 670 LEU cc_start: 0.7988 (mt) cc_final: 0.7754 (mt) REVERT: B 680 GLN cc_start: 0.7738 (mt0) cc_final: 0.7404 (mp10) REVERT: C 428 ASP cc_start: 0.5639 (OUTLIER) cc_final: 0.5392 (m-30) REVERT: C 448 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 452 ASP cc_start: 0.7108 (m-30) cc_final: 0.6876 (m-30) REVERT: C 489 SER cc_start: 0.8527 (m) cc_final: 0.8156 (p) REVERT: C 521 LYS cc_start: 0.8301 (mttt) cc_final: 0.8083 (mttt) REVERT: C 672 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7531 (mt-10) REVERT: C 676 SER cc_start: 0.8846 (t) cc_final: 0.8453 (m) REVERT: D 429 GLU cc_start: 0.8104 (pm20) cc_final: 0.7865 (pm20) REVERT: D 432 LEU cc_start: 0.8619 (mt) cc_final: 0.8368 (mt) REVERT: D 489 SER cc_start: 0.8402 (t) cc_final: 0.7974 (p) REVERT: D 492 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.7852 (ttm-80) REVERT: D 519 MET cc_start: 0.7429 (tpt) cc_final: 0.6896 (tpt) REVERT: D 541 LEU cc_start: 0.8425 (tt) cc_final: 0.8200 (mt) REVERT: D 556 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7747 (mt-10) REVERT: D 568 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7494 (mtt-85) REVERT: D 637 SER cc_start: 0.8626 (m) cc_final: 0.8401 (t) REVERT: D 667 ASP cc_start: 0.7103 (p0) cc_final: 0.6877 (p0) REVERT: D 671 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7876 (mtmt) REVERT: E 464 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7684 (mmt90) REVERT: E 470 SER cc_start: 0.8597 (t) cc_final: 0.8393 (p) REVERT: E 500 MET cc_start: 0.8489 (mmm) cc_final: 0.8192 (mmt) REVERT: E 505 GLU cc_start: 0.7731 (mp0) cc_final: 0.7435 (mp0) REVERT: E 561 GLU cc_start: 0.7417 (mp0) cc_final: 0.7164 (mp0) REVERT: E 672 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7185 (mt-10) REVERT: E 680 GLN cc_start: 0.8271 (tp40) cc_final: 0.7947 (tp-100) REVERT: E 685 GLU cc_start: 0.7758 (mp0) cc_final: 0.7291 (mp0) REVERT: F 460 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7978 (pp) REVERT: F 537 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7499 (tp30) REVERT: F 556 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7561 (mt-10) REVERT: F 581 MET cc_start: 0.8388 (mtt) cc_final: 0.8146 (mtp) REVERT: F 611 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.8284 (ttp80) REVERT: F 613 ASP cc_start: 0.7754 (m-30) cc_final: 0.7532 (m-30) REVERT: F 633 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5598 (tt0) REVERT: F 661 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7493 (mtm110) REVERT: F 679 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7961 (ttm110) REVERT: F 688 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7413 (mp0) outliers start: 65 outliers final: 30 residues processed: 507 average time/residue: 0.7729 time to fit residues: 418.1101 Evaluate side-chains 506 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 468 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 684 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 459 VAL 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 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 671 LYS Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 697 LYS 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 F residue 438 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 460 LEU 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 113 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 156 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 569 GLN C 680 GLN D 455 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122098 restraints weight = 16465.092| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.80 r_work: 0.3442 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13290 Z= 0.175 Angle : 0.544 7.797 17943 Z= 0.272 Chirality : 0.038 0.123 2030 Planarity : 0.005 0.048 2341 Dihedral : 4.944 56.415 1797 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.22 % Favored : 97.16 % Rotamer: Outliers : 5.32 % Allowed : 23.93 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.21), residues: 1622 helix: 2.65 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -1.90 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 539 TYR 0.011 0.002 TYR F 686 PHE 0.023 0.002 PHE E 450 TRP 0.005 0.001 TRP C 551 HIS 0.004 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00418 (13290) covalent geometry : angle 0.54437 (17943) hydrogen bonds : bond 0.05223 ( 985) hydrogen bonds : angle 3.56834 ( 2925) *********************** 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 543 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 465 time to evaluate : 0.547 Fit side-chains REVERT: A 432 LEU cc_start: 0.8155 (mp) cc_final: 0.7211 (mt) REVERT: A 436 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7056 (mp0) REVERT: A 487 ASP cc_start: 0.7687 (m-30) cc_final: 0.7176 (m-30) REVERT: A 496 PRO cc_start: 0.8685 (Cg_exo) cc_final: 0.8479 (Cg_endo) REVERT: A 505 GLU cc_start: 0.8011 (mp0) cc_final: 0.7752 (mp0) REVERT: A 520 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7192 (mp0) REVERT: A 581 MET cc_start: 0.8396 (mtt) cc_final: 0.8137 (mtt) REVERT: A 670 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7856 (mp) REVERT: A 672 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7121 (mt-10) REVERT: A 684 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7087 (mm) REVERT: A 688 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 447 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8159 (mpt180) REVERT: B 448 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: B 505 GLU cc_start: 0.7951 (mp0) cc_final: 0.7732 (mp0) REVERT: B 537 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7308 (tp30) REVERT: B 539 ARG cc_start: 0.8309 (ttt90) cc_final: 0.8057 (ttt-90) REVERT: B 633 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5392 (tt0) REVERT: B 661 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7666 (ttp-110) REVERT: B 667 ASP cc_start: 0.6531 (p0) cc_final: 0.6189 (p0) REVERT: B 670 LEU cc_start: 0.7999 (mt) cc_final: 0.7743 (mt) REVERT: B 672 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7168 (mt-10) REVERT: B 680 GLN cc_start: 0.7794 (mt0) cc_final: 0.7444 (mp10) REVERT: C 448 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 452 ASP cc_start: 0.7091 (m-30) cc_final: 0.6870 (m-30) REVERT: C 672 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 676 SER cc_start: 0.8824 (t) cc_final: 0.8440 (m) REVERT: D 432 LEU cc_start: 0.8610 (mt) cc_final: 0.8288 (mt) REVERT: D 487 ASP cc_start: 0.7290 (m-30) cc_final: 0.6992 (m-30) REVERT: D 489 SER cc_start: 0.8413 (t) cc_final: 0.7957 (p) REVERT: D 492 ARG cc_start: 0.8285 (tpp-160) cc_final: 0.7956 (ttm-80) REVERT: D 541 LEU cc_start: 0.8440 (tt) cc_final: 0.8220 (mt) REVERT: D 556 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 568 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7526 (mtt-85) REVERT: D 637 SER cc_start: 0.8728 (m) cc_final: 0.8496 (t) REVERT: D 667 ASP cc_start: 0.7151 (p0) cc_final: 0.6886 (p0) REVERT: D 671 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7884 (mtmt) REVERT: E 464 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7751 (mmt90) REVERT: E 470 SER cc_start: 0.8596 (t) cc_final: 0.8364 (p) REVERT: E 500 MET cc_start: 0.8488 (mmm) cc_final: 0.8215 (mmt) REVERT: E 505 GLU cc_start: 0.7780 (mp0) cc_final: 0.7495 (mp0) REVERT: E 506 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: E 561 GLU cc_start: 0.7428 (mp0) cc_final: 0.7189 (mp0) REVERT: E 672 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7165 (mt-10) REVERT: E 680 GLN cc_start: 0.8271 (tp40) cc_final: 0.7925 (tp-100) REVERT: E 685 GLU cc_start: 0.7793 (mp0) cc_final: 0.7236 (mp0) REVERT: F 537 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7396 (tp30) REVERT: F 556 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7548 (mt-10) REVERT: F 581 MET cc_start: 0.8415 (mtt) cc_final: 0.8167 (mtp) REVERT: F 611 ARG cc_start: 0.8569 (ttp-170) cc_final: 0.8348 (ttp80) REVERT: F 613 ASP cc_start: 0.7812 (m-30) cc_final: 0.7609 (m-30) REVERT: F 633 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5590 (tt0) REVERT: F 658 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: F 679 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7993 (ttm110) REVERT: F 688 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7428 (mt-10) outliers start: 78 outliers final: 46 residues processed: 513 average time/residue: 0.7586 time to fit residues: 415.4653 Evaluate side-chains 517 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 462 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 684 ILE Chi-restraints excluded: chain A residue 688 GLU 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 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 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 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 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 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 527 ASP Chi-restraints excluded: chain F residue 529 ARG 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 125 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 680 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121536 restraints weight = 16518.559| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.80 r_work: 0.3433 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13290 Z= 0.194 Angle : 0.569 10.070 17943 Z= 0.283 Chirality : 0.039 0.130 2030 Planarity : 0.005 0.049 2341 Dihedral : 4.678 49.663 1795 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.68 % Allowed : 2.47 % Favored : 96.86 % Rotamer: Outliers : 4.98 % Allowed : 24.88 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.21), residues: 1622 helix: 2.59 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -1.88 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 661 TYR 0.012 0.002 TYR B 614 PHE 0.023 0.002 PHE E 450 TRP 0.005 0.001 TRP C 551 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00467 (13290) covalent geometry : angle 0.56935 (17943) hydrogen bonds : bond 0.05436 ( 985) hydrogen bonds : angle 3.57671 ( 2925) *********************** 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 545 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 472 time to evaluate : 0.522 Fit side-chains REVERT: A 432 LEU cc_start: 0.8172 (mp) cc_final: 0.7592 (mt) REVERT: A 436 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7134 (mp0) REVERT: A 487 ASP cc_start: 0.7719 (m-30) cc_final: 0.7238 (m-30) REVERT: A 496 PRO cc_start: 0.8685 (Cg_exo) cc_final: 0.8484 (Cg_endo) REVERT: A 505 GLU cc_start: 0.8030 (mp0) cc_final: 0.7781 (mp0) REVERT: A 520 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7083 (mp0) REVERT: A 581 MET cc_start: 0.8439 (mtt) cc_final: 0.8156 (mtt) REVERT: A 613 ASP cc_start: 0.8113 (m-30) cc_final: 0.7891 (m-30) REVERT: A 670 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 672 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7083 (mt-10) REVERT: A 684 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 688 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 447 ARG cc_start: 0.8408 (mtt90) cc_final: 0.8142 (mpt180) REVERT: B 448 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: B 505 GLU cc_start: 0.7979 (mp0) cc_final: 0.7753 (mp0) REVERT: B 537 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7338 (tp30) REVERT: B 539 ARG cc_start: 0.8298 (ttt90) cc_final: 0.8040 (ttt-90) REVERT: B 633 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.5320 (tt0) REVERT: B 661 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7729 (ttp-110) REVERT: B 667 ASP cc_start: 0.6600 (p0) cc_final: 0.6239 (p0) REVERT: B 670 LEU cc_start: 0.8038 (mt) cc_final: 0.7787 (mt) REVERT: B 672 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 680 GLN cc_start: 0.7826 (mt0) cc_final: 0.7465 (mp10) REVERT: C 448 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: C 452 ASP cc_start: 0.7089 (m-30) cc_final: 0.6852 (m-30) REVERT: C 519 MET cc_start: 0.7945 (mtt) cc_final: 0.7673 (mtm) REVERT: C 672 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 676 SER cc_start: 0.8825 (t) cc_final: 0.8439 (m) REVERT: D 487 ASP cc_start: 0.7297 (m-30) cc_final: 0.6999 (m-30) REVERT: D 541 LEU cc_start: 0.8443 (tt) cc_final: 0.8225 (mt) REVERT: D 548 ASP cc_start: 0.7981 (t70) cc_final: 0.7694 (t0) REVERT: D 556 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7643 (mt-10) REVERT: D 568 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7494 (mtt-85) REVERT: D 613 ASP cc_start: 0.8041 (m-30) cc_final: 0.7785 (m-30) REVERT: D 667 ASP cc_start: 0.7187 (p0) cc_final: 0.6967 (p0) REVERT: D 671 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7899 (mtmt) REVERT: E 464 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.7773 (mmt90) REVERT: E 470 SER cc_start: 0.8615 (t) cc_final: 0.8393 (p) REVERT: E 500 MET cc_start: 0.8499 (mmm) cc_final: 0.8217 (mmt) REVERT: E 505 GLU cc_start: 0.7774 (mp0) cc_final: 0.7491 (mp0) REVERT: E 506 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: E 561 GLU cc_start: 0.7413 (mp0) cc_final: 0.7202 (mp0) REVERT: E 672 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7144 (mt-10) REVERT: E 680 GLN cc_start: 0.8297 (tp40) cc_final: 0.7947 (tp-100) REVERT: E 685 GLU cc_start: 0.7797 (mp0) cc_final: 0.7315 (mp0) REVERT: F 537 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7449 (tp30) REVERT: F 556 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7526 (mt-10) REVERT: F 581 MET cc_start: 0.8425 (mtt) cc_final: 0.8168 (mtp) REVERT: F 613 ASP cc_start: 0.7875 (m-30) cc_final: 0.7651 (m-30) REVERT: F 633 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5544 (tt0) REVERT: F 658 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: F 679 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7904 (ttm-80) REVERT: F 688 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7399 (mt-10) outliers start: 73 outliers final: 48 residues processed: 516 average time/residue: 0.7354 time to fit residues: 404.9320 Evaluate side-chains 531 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 473 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 684 ILE Chi-restraints excluded: chain A residue 688 GLU 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 618 THR 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 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 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 527 ASP Chi-restraints excluded: chain F residue 529 ARG 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 131 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 150 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 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 C 680 GLN D 545 GLN D 647 GLN E 466 ASN E 512 ASN F 512 ASN F 524 GLN F 545 GLN F 569 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122132 restraints weight = 16497.398| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.81 r_work: 0.3448 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13290 Z= 0.165 Angle : 0.559 9.024 17943 Z= 0.280 Chirality : 0.038 0.127 2030 Planarity : 0.005 0.057 2341 Dihedral : 4.576 47.622 1793 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.22 % Favored : 97.16 % Rotamer: Outliers : 5.04 % Allowed : 25.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.21), residues: 1622 helix: 2.66 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -1.83 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 661 TYR 0.012 0.001 TYR B 614 PHE 0.022 0.001 PHE E 450 TRP 0.003 0.001 TRP B 457 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00390 (13290) covalent geometry : angle 0.55938 (17943) hydrogen bonds : bond 0.05104 ( 985) hydrogen bonds : angle 3.51475 ( 2925) *********************** 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 544 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 470 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8160 (mp) cc_final: 0.7210 (mt) REVERT: A 436 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7051 (mp0) REVERT: A 487 ASP cc_start: 0.7695 (m-30) cc_final: 0.7228 (m-30) REVERT: A 505 GLU cc_start: 0.8006 (mp0) cc_final: 0.7742 (mp0) REVERT: A 520 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7212 (mp0) REVERT: A 521 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8022 (mtpt) REVERT: A 581 MET cc_start: 0.8417 (mtt) cc_final: 0.8156 (mtt) REVERT: A 613 ASP cc_start: 0.8088 (m-30) cc_final: 0.7867 (m-30) REVERT: A 670 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 672 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7074 (mt-10) REVERT: B 447 ARG cc_start: 0.8397 (mtt90) cc_final: 0.8123 (mpt180) REVERT: B 448 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: B 505 GLU cc_start: 0.7961 (mp0) cc_final: 0.7742 (mp0) REVERT: B 537 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7290 (tp30) REVERT: B 539 ARG cc_start: 0.8304 (ttt90) cc_final: 0.8034 (ttt-90) REVERT: B 633 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5398 (tt0) REVERT: B 658 GLN cc_start: 0.8134 (tp40) cc_final: 0.7912 (tp40) REVERT: B 661 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7684 (ttm-80) REVERT: B 667 ASP cc_start: 0.6601 (p0) cc_final: 0.6231 (p0) REVERT: B 670 LEU cc_start: 0.8036 (mt) cc_final: 0.7796 (mt) REVERT: B 672 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 680 GLN cc_start: 0.7799 (mt0) cc_final: 0.7426 (mp10) REVERT: C 448 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: C 452 ASP cc_start: 0.7088 (m-30) cc_final: 0.6849 (m-30) REVERT: C 672 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7544 (mt-10) REVERT: C 676 SER cc_start: 0.8830 (t) cc_final: 0.8458 (m) REVERT: C 679 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7677 (mpp80) REVERT: C 680 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7376 (tm-30) REVERT: C 696 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: D 432 LEU cc_start: 0.8613 (mt) cc_final: 0.8247 (mt) REVERT: D 487 ASP cc_start: 0.7342 (m-30) cc_final: 0.7037 (m-30) REVERT: D 541 LEU cc_start: 0.8439 (tt) cc_final: 0.8219 (mt) REVERT: D 548 ASP cc_start: 0.7978 (t70) cc_final: 0.7704 (t0) REVERT: D 556 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7608 (mt-10) REVERT: D 568 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7548 (mtt-85) REVERT: D 611 ARG cc_start: 0.8580 (ttt-90) cc_final: 0.8258 (ttt180) REVERT: D 667 ASP cc_start: 0.7175 (p0) cc_final: 0.6943 (p0) REVERT: D 671 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7901 (mtmt) REVERT: E 470 SER cc_start: 0.8585 (t) cc_final: 0.8356 (p) REVERT: E 500 MET cc_start: 0.8506 (mmm) cc_final: 0.8243 (mmt) REVERT: E 505 GLU cc_start: 0.7770 (mp0) cc_final: 0.7498 (mp0) REVERT: E 506 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: E 561 GLU cc_start: 0.7369 (mp0) cc_final: 0.7152 (mp0) REVERT: E 672 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7154 (mt-10) REVERT: E 680 GLN cc_start: 0.8299 (tp40) cc_final: 0.7949 (tp-100) REVERT: E 685 GLU cc_start: 0.7784 (mp0) cc_final: 0.7298 (mp0) REVERT: F 537 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7486 (tp30) REVERT: F 556 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 581 MET cc_start: 0.8403 (mtt) cc_final: 0.8150 (mtp) REVERT: F 583 VAL cc_start: 0.8070 (t) cc_final: 0.7801 (m) REVERT: F 611 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.8345 (ttp80) REVERT: F 613 ASP cc_start: 0.7843 (m-30) cc_final: 0.7639 (m-30) REVERT: F 658 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: F 661 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7537 (ttm110) REVERT: F 675 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8297 (tt) REVERT: F 679 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7932 (ttm110) REVERT: F 688 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7350 (mt-10) outliers start: 74 outliers final: 49 residues processed: 508 average time/residue: 0.7405 time to fit residues: 401.6443 Evaluate side-chains 525 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 465 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 688 GLU 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 679 ARG 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 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 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 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 527 ASP Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 696 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 0.0980 chunk 130 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 1 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 A 658 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122395 restraints weight = 16433.479| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.80 r_work: 0.3446 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13290 Z= 0.160 Angle : 0.552 8.532 17943 Z= 0.278 Chirality : 0.037 0.127 2030 Planarity : 0.005 0.051 2341 Dihedral : 4.282 45.974 1790 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.28 % Favored : 97.10 % Rotamer: Outliers : 5.18 % Allowed : 25.49 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.21), residues: 1622 helix: 2.71 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -1.80 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 661 TYR 0.012 0.002 TYR B 614 PHE 0.023 0.001 PHE E 450 TRP 0.003 0.001 TRP B 457 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00377 (13290) covalent geometry : angle 0.55195 (17943) hydrogen bonds : bond 0.05008 ( 985) hydrogen bonds : angle 3.50626 ( 2925) *********************** 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 546 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 470 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8179 (mp) cc_final: 0.7202 (mt) REVERT: A 436 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7036 (mp0) REVERT: A 487 ASP cc_start: 0.7698 (m-30) cc_final: 0.7239 (m-30) REVERT: A 505 GLU cc_start: 0.8006 (mp0) cc_final: 0.7735 (mp0) REVERT: A 520 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7213 (mp0) REVERT: A 521 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.8020 (mtpt) REVERT: A 581 MET cc_start: 0.8400 (mtt) cc_final: 0.8163 (mtt) REVERT: A 613 ASP cc_start: 0.8095 (m-30) cc_final: 0.7856 (m-30) REVERT: A 670 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7827 (mp) REVERT: A 672 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 447 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8119 (mpt180) REVERT: B 448 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: B 505 GLU cc_start: 0.7959 (mp0) cc_final: 0.7750 (mp0) REVERT: B 537 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7301 (tp30) REVERT: B 539 ARG cc_start: 0.8285 (ttt90) cc_final: 0.8029 (ttt-90) REVERT: B 633 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5409 (tt0) REVERT: B 661 ARG cc_start: 0.7968 (tpp80) cc_final: 0.7697 (ttm-80) REVERT: B 667 ASP cc_start: 0.6589 (p0) cc_final: 0.6226 (p0) REVERT: B 670 LEU cc_start: 0.8027 (mt) cc_final: 0.7784 (mt) REVERT: B 672 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 680 GLN cc_start: 0.7783 (mt0) cc_final: 0.7400 (mp10) REVERT: B 688 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7196 (mp0) REVERT: C 448 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: C 452 ASP cc_start: 0.7075 (m-30) cc_final: 0.6840 (m-30) REVERT: C 672 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7572 (mt-10) REVERT: C 676 SER cc_start: 0.8828 (t) cc_final: 0.8452 (m) REVERT: C 679 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7660 (mpp80) REVERT: C 696 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: D 432 LEU cc_start: 0.8600 (mt) cc_final: 0.8240 (mt) REVERT: D 487 ASP cc_start: 0.7343 (m-30) cc_final: 0.7046 (m-30) REVERT: D 489 SER cc_start: 0.8453 (t) cc_final: 0.8086 (p) REVERT: D 492 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7988 (ttm-80) REVERT: D 541 LEU cc_start: 0.8428 (tt) cc_final: 0.8202 (mt) REVERT: D 548 ASP cc_start: 0.7958 (t70) cc_final: 0.7679 (t0) REVERT: D 556 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7609 (mt-10) REVERT: D 568 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7549 (mtt-85) REVERT: D 611 ARG cc_start: 0.8574 (ttt-90) cc_final: 0.8263 (ttt180) REVERT: D 667 ASP cc_start: 0.7177 (p0) cc_final: 0.6947 (p0) REVERT: D 671 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7891 (mtmt) REVERT: E 500 MET cc_start: 0.8500 (mmm) cc_final: 0.8240 (mmt) REVERT: E 505 GLU cc_start: 0.7752 (mp0) cc_final: 0.7473 (mp0) REVERT: E 506 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: E 512 ASN cc_start: 0.8383 (m-40) cc_final: 0.8144 (m110) REVERT: E 561 GLU cc_start: 0.7412 (mp0) cc_final: 0.7202 (mp0) REVERT: E 672 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7163 (mt-10) REVERT: E 680 GLN cc_start: 0.8315 (tp40) cc_final: 0.7958 (tp-100) REVERT: E 685 GLU cc_start: 0.7794 (mp0) cc_final: 0.7310 (mp0) REVERT: E 704 SER cc_start: 0.7981 (t) cc_final: 0.7610 (p) REVERT: F 537 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7389 (tp30) REVERT: F 556 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7570 (mt-10) REVERT: F 581 MET cc_start: 0.8401 (mtt) cc_final: 0.8151 (mtp) REVERT: F 583 VAL cc_start: 0.8058 (t) cc_final: 0.7789 (m) REVERT: F 611 ARG cc_start: 0.8567 (ttp-170) cc_final: 0.8351 (ttp80) REVERT: F 658 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: F 661 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7522 (ttm110) REVERT: F 675 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8209 (tt) REVERT: F 679 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7855 (ttm170) REVERT: F 688 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7316 (mt-10) outliers start: 76 outliers final: 49 residues processed: 512 average time/residue: 0.7303 time to fit residues: 399.2292 Evaluate side-chains 523 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 463 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 688 GLU 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 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 679 ARG 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 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 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 Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 696 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 160 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 154 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 545 GLN B 512 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 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 = 0.3727 r_free = 0.3727 target = 0.133673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121345 restraints weight = 16235.532| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.77 r_work: 0.3436 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13290 Z= 0.202 Angle : 0.594 10.747 17943 Z= 0.298 Chirality : 0.040 0.141 2030 Planarity : 0.005 0.055 2341 Dihedral : 4.361 46.916 1790 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.65 % Favored : 96.73 % Rotamer: Outliers : 5.32 % Allowed : 25.84 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.21), residues: 1622 helix: 2.60 (0.14), residues: 1291 sheet: None (None), residues: 0 loop : -1.78 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 539 TYR 0.013 0.002 TYR A 614 PHE 0.025 0.002 PHE E 450 TRP 0.006 0.001 TRP C 551 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00487 (13290) covalent geometry : angle 0.59419 (17943) hydrogen bonds : bond 0.05512 ( 985) hydrogen bonds : angle 3.59022 ( 2925) *********************** 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 552 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 474 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8194 (mp) cc_final: 0.7554 (mt) REVERT: A 436 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7132 (mp0) REVERT: A 487 ASP cc_start: 0.7720 (m-30) cc_final: 0.7273 (m-30) REVERT: A 505 GLU cc_start: 0.7952 (mp0) cc_final: 0.7701 (mp0) REVERT: A 520 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7207 (mp0) REVERT: A 521 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8022 (mtpt) REVERT: A 581 MET cc_start: 0.8420 (mtt) cc_final: 0.8169 (mtt) REVERT: A 613 ASP cc_start: 0.8098 (m-30) cc_final: 0.7854 (m-30) REVERT: A 670 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 672 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7037 (mt-10) REVERT: B 447 ARG cc_start: 0.8414 (mtt90) cc_final: 0.8149 (mpt180) REVERT: B 448 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: B 470 SER cc_start: 0.8604 (t) cc_final: 0.8303 (p) REVERT: B 505 GLU cc_start: 0.7954 (mp0) cc_final: 0.7729 (mp0) REVERT: B 537 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7321 (tp30) REVERT: B 539 ARG cc_start: 0.8296 (ttt90) cc_final: 0.8042 (ttt-90) REVERT: B 633 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5522 (tt0) REVERT: B 658 GLN cc_start: 0.8152 (tp40) cc_final: 0.7931 (tp40) REVERT: B 661 ARG cc_start: 0.7952 (tpp80) cc_final: 0.7669 (ttm-80) REVERT: B 667 ASP cc_start: 0.6630 (p0) cc_final: 0.6279 (p0) REVERT: B 670 LEU cc_start: 0.8051 (mt) cc_final: 0.7818 (mt) REVERT: B 672 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 680 GLN cc_start: 0.7802 (mt0) cc_final: 0.7424 (mp10) REVERT: C 448 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: C 452 ASP cc_start: 0.7084 (m-30) cc_final: 0.6852 (m-30) REVERT: C 672 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 676 SER cc_start: 0.8845 (t) cc_final: 0.8470 (m) REVERT: C 679 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7686 (mpp80) REVERT: C 680 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7373 (tm130) REVERT: C 696 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: D 432 LEU cc_start: 0.8609 (mt) cc_final: 0.8223 (mt) REVERT: D 487 ASP cc_start: 0.7351 (m-30) cc_final: 0.7039 (m-30) REVERT: D 541 LEU cc_start: 0.8435 (tt) cc_final: 0.8220 (mt) REVERT: D 556 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7570 (mt-10) REVERT: D 568 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7490 (mtt-85) REVERT: D 611 ARG cc_start: 0.8553 (ttt-90) cc_final: 0.8230 (ttt180) REVERT: D 667 ASP cc_start: 0.7176 (p0) cc_final: 0.6934 (p0) REVERT: D 671 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7886 (mtmt) REVERT: E 487 ASP cc_start: 0.7679 (m-30) cc_final: 0.7323 (m-30) REVERT: E 500 MET cc_start: 0.8495 (mmm) cc_final: 0.8240 (mmt) REVERT: E 506 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: E 672 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7111 (mt-10) REVERT: E 680 GLN cc_start: 0.8300 (tp40) cc_final: 0.7940 (tp-100) REVERT: E 685 GLU cc_start: 0.7778 (mp0) cc_final: 0.7346 (mp0) REVERT: E 704 SER cc_start: 0.7959 (t) cc_final: 0.7593 (p) REVERT: F 537 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7470 (tp30) REVERT: F 556 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7541 (mt-10) REVERT: F 581 MET cc_start: 0.8400 (mtt) cc_final: 0.8158 (mtp) REVERT: F 583 VAL cc_start: 0.8038 (t) cc_final: 0.7759 (m) REVERT: F 617 LEU cc_start: 0.8597 (tp) cc_final: 0.8357 (mt) REVERT: F 658 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: F 675 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8233 (tt) REVERT: F 679 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7933 (ttm110) REVERT: F 688 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7340 (mt-10) outliers start: 78 outliers final: 49 residues processed: 515 average time/residue: 0.7704 time to fit residues: 423.0828 Evaluate side-chains 522 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 462 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 688 GLU 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 529 ARG 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 588 VAL Chi-restraints excluded: chain C residue 604 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 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 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 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 Chi-restraints excluded: chain F residue 675 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 29 optimal weight: 0.4980 chunk 23 optimal weight: 0.0270 chunk 90 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 151 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 117 optimal weight: 0.0870 chunk 46 optimal weight: 0.4980 overall best weight: 0.2014 ------------------------------------------------------------------------------- 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 D 499 HIS 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 = 0.3763 r_free = 0.3763 target = 0.136460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124138 restraints weight = 16464.638| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.79 r_work: 0.3468 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13290 Z= 0.119 Angle : 0.558 11.361 17943 Z= 0.278 Chirality : 0.036 0.120 2030 Planarity : 0.005 0.047 2341 Dihedral : 4.190 45.026 1790 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.16 % Favored : 97.23 % Rotamer: Outliers : 3.89 % Allowed : 27.68 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.21), residues: 1622 helix: 2.82 (0.14), residues: 1301 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 495 TYR 0.011 0.001 TYR A 614 PHE 0.024 0.001 PHE E 450 TRP 0.006 0.001 TRP C 551 HIS 0.004 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00259 (13290) covalent geometry : angle 0.55785 (17943) hydrogen bonds : bond 0.04316 ( 985) hydrogen bonds : angle 3.42955 ( 2925) *********************** 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 524 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 467 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8126 (mp) cc_final: 0.6994 (mt) REVERT: A 436 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7024 (mp0) REVERT: A 487 ASP cc_start: 0.7628 (m-30) cc_final: 0.7193 (m-30) REVERT: A 505 GLU cc_start: 0.7922 (mp0) cc_final: 0.7660 (mp0) REVERT: A 520 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7148 (mp0) REVERT: A 613 ASP cc_start: 0.8020 (m-30) cc_final: 0.7738 (m-30) REVERT: A 670 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 672 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 447 ARG cc_start: 0.8382 (mtt90) cc_final: 0.8103 (mpt180) REVERT: B 537 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7270 (tp30) REVERT: B 539 ARG cc_start: 0.8306 (ttt90) cc_final: 0.8056 (ttt-90) REVERT: B 633 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5520 (tt0) REVERT: B 661 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7665 (ttm-80) REVERT: B 667 ASP cc_start: 0.6630 (p0) cc_final: 0.6251 (p0) REVERT: B 670 LEU cc_start: 0.7957 (mt) cc_final: 0.7742 (mt) REVERT: B 672 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7164 (mt-10) REVERT: B 680 GLN cc_start: 0.7760 (mt0) cc_final: 0.7376 (mp10) REVERT: C 448 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: C 452 ASP cc_start: 0.7091 (m-30) cc_final: 0.6845 (m-30) REVERT: C 672 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 676 SER cc_start: 0.8817 (t) cc_final: 0.8402 (m) REVERT: C 679 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7909 (mtm-85) REVERT: C 696 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: D 432 LEU cc_start: 0.8576 (mt) cc_final: 0.8197 (mt) REVERT: D 487 ASP cc_start: 0.7316 (m-30) cc_final: 0.6998 (m-30) REVERT: D 489 SER cc_start: 0.8460 (t) cc_final: 0.8111 (p) REVERT: D 541 LEU cc_start: 0.8385 (tt) cc_final: 0.8158 (mt) REVERT: D 556 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7597 (mt-10) REVERT: D 565 ASP cc_start: 0.7584 (m-30) cc_final: 0.7341 (m-30) REVERT: D 568 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7548 (mtt-85) REVERT: D 667 ASP cc_start: 0.7147 (p0) cc_final: 0.6915 (p0) REVERT: D 671 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7867 (mtmt) REVERT: E 500 MET cc_start: 0.8426 (mmm) cc_final: 0.8138 (mmt) REVERT: E 505 GLU cc_start: 0.7708 (mp0) cc_final: 0.7454 (mp0) REVERT: E 512 ASN cc_start: 0.8349 (m-40) cc_final: 0.8065 (m110) REVERT: E 672 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7047 (mt-10) REVERT: E 680 GLN cc_start: 0.8310 (tp40) cc_final: 0.7936 (tp-100) REVERT: E 685 GLU cc_start: 0.7773 (mp0) cc_final: 0.7230 (mp0) REVERT: F 537 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7420 (tp30) REVERT: F 556 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7567 (mt-10) REVERT: F 581 MET cc_start: 0.8368 (mtt) cc_final: 0.8132 (mtt) REVERT: F 583 VAL cc_start: 0.8088 (t) cc_final: 0.7818 (m) REVERT: F 611 ARG cc_start: 0.8570 (ttp-170) cc_final: 0.8364 (ttp80) REVERT: F 661 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7500 (ttm110) REVERT: F 679 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7758 (ttm170) REVERT: F 688 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7266 (mt-10) outliers start: 57 outliers final: 36 residues processed: 500 average time/residue: 0.7422 time to fit residues: 397.0596 Evaluate side-chains 512 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 470 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR 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 688 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 529 ARG 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 679 ARG Chi-restraints excluded: chain C residue 696 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 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 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 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 527 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 0.0870 chunk 104 optimal weight: 0.2980 chunk 91 optimal weight: 0.0980 chunk 16 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 545 GLN B 512 ASN B 545 GLN C 545 GLN C 680 GLN D 647 GLN E 466 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 = 0.3779 r_free = 0.3779 target = 0.137877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125501 restraints weight = 16510.102| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.80 r_work: 0.3489 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13290 Z= 0.113 Angle : 0.559 11.942 17943 Z= 0.280 Chirality : 0.036 0.136 2030 Planarity : 0.005 0.047 2341 Dihedral : 3.933 43.736 1788 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.68 % Allowed : 1.91 % Favored : 97.41 % Rotamer: Outliers : 3.34 % Allowed : 28.77 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.21), residues: 1622 helix: 2.93 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 539 TYR 0.011 0.001 TYR E 614 PHE 0.024 0.001 PHE E 450 TRP 0.006 0.001 TRP C 551 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00240 (13290) covalent geometry : angle 0.55926 (17943) hydrogen bonds : bond 0.03879 ( 985) hydrogen bonds : angle 3.38541 ( 2925) ********************** 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 520 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 471 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8088 (mp) cc_final: 0.7274 (mt) REVERT: A 436 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7051 (mt-10) REVERT: A 487 ASP cc_start: 0.7578 (m-30) cc_final: 0.7108 (m-30) REVERT: A 505 GLU cc_start: 0.7893 (mp0) cc_final: 0.7627 (mp0) REVERT: A 516 ILE cc_start: 0.7805 (mm) cc_final: 0.7139 (mp) REVERT: A 520 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7063 (mp0) REVERT: A 670 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7771 (mp) REVERT: A 672 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 447 ARG cc_start: 0.8377 (mtt90) cc_final: 0.8088 (mpt180) REVERT: B 537 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7228 (tp30) REVERT: B 539 ARG cc_start: 0.8277 (ttt90) cc_final: 0.8026 (ttt-90) REVERT: B 633 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5514 (tt0) REVERT: B 661 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7646 (ttm-80) REVERT: B 667 ASP cc_start: 0.6574 (p0) cc_final: 0.6183 (p0) REVERT: B 670 LEU cc_start: 0.7950 (mt) cc_final: 0.7729 (mt) REVERT: B 672 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 680 GLN cc_start: 0.7756 (mt0) cc_final: 0.7363 (mp10) REVERT: C 429 GLU cc_start: 0.8092 (pm20) cc_final: 0.7566 (pm20) REVERT: C 448 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: C 452 ASP cc_start: 0.7060 (m-30) cc_final: 0.6825 (m-30) REVERT: C 672 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7533 (mt-10) REVERT: C 676 SER cc_start: 0.8815 (t) cc_final: 0.8397 (m) REVERT: C 679 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7870 (mtm-85) REVERT: C 680 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 696 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: D 432 LEU cc_start: 0.8489 (mt) cc_final: 0.8128 (mt) REVERT: D 487 ASP cc_start: 0.7276 (m-30) cc_final: 0.6960 (m-30) REVERT: D 489 SER cc_start: 0.8416 (t) cc_final: 0.8089 (p) REVERT: D 492 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7942 (ttm-80) REVERT: D 541 LEU cc_start: 0.8350 (tt) cc_final: 0.8097 (mt) REVERT: D 556 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7618 (mt-10) REVERT: D 565 ASP cc_start: 0.7611 (m-30) cc_final: 0.7354 (m-30) REVERT: D 568 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7563 (mtt-85) REVERT: D 613 ASP cc_start: 0.7789 (m-30) cc_final: 0.7492 (m-30) REVERT: D 658 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7984 (mm-40) REVERT: D 667 ASP cc_start: 0.7120 (p0) cc_final: 0.6849 (p0) REVERT: D 671 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7855 (mtmt) REVERT: E 500 MET cc_start: 0.8452 (mmm) cc_final: 0.8185 (mmt) REVERT: E 505 GLU cc_start: 0.7707 (mp0) cc_final: 0.7466 (mp0) REVERT: E 512 ASN cc_start: 0.8399 (m-40) cc_final: 0.8154 (m110) REVERT: E 537 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7859 (mp0) REVERT: E 672 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7008 (mt-10) REVERT: E 680 GLN cc_start: 0.8363 (tp40) cc_final: 0.7975 (tp-100) REVERT: E 688 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: F 537 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7400 (tp30) REVERT: F 556 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7585 (mt-10) REVERT: F 582 MET cc_start: 0.8301 (mtp) cc_final: 0.8087 (mtt) REVERT: F 583 VAL cc_start: 0.8118 (t) cc_final: 0.7863 (m) REVERT: F 611 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8226 (tmm160) REVERT: F 633 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5818 (tt0) REVERT: F 661 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7520 (ttm110) REVERT: F 679 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7742 (ttm170) REVERT: F 688 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7191 (mt-10) outliers start: 49 outliers final: 31 residues processed: 497 average time/residue: 0.7791 time to fit residues: 412.9530 Evaluate side-chains 498 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 459 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 688 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 504 THR 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 588 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 679 ARG Chi-restraints excluded: chain C residue 696 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 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 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 671 LYS Chi-restraints excluded: chain E residue 688 GLU Chi-restraints excluded: chain F residue 429 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 577 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 633 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 79 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 C 545 GLN D 512 ASN D 545 GLN D 647 GLN E 466 ASN E 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123476 restraints weight = 16334.387| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.80 r_work: 0.3467 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13290 Z= 0.147 Angle : 0.606 12.911 17943 Z= 0.301 Chirality : 0.038 0.179 2030 Planarity : 0.005 0.058 2341 Dihedral : 3.869 44.537 1786 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 1.91 % Favored : 97.41 % Rotamer: Outliers : 3.20 % Allowed : 28.97 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.04 (0.21), residues: 1622 helix: 2.83 (0.14), residues: 1297 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 661 TYR 0.013 0.002 TYR A 614 PHE 0.026 0.001 PHE E 450 TRP 0.003 0.001 TRP D 457 HIS 0.004 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00347 (13290) covalent geometry : angle 0.60638 (17943) hydrogen bonds : bond 0.04502 ( 985) hydrogen bonds : angle 3.45916 ( 2925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6722.65 seconds wall clock time: 114 minutes 45.71 seconds (6885.71 seconds total)