Starting phenix.real_space_refine on Sat Jul 4 08:52:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnm_26014/07_2026/7tnm_26014.map" } resolution = 4.74 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= 0.002 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12570 2.51 5 N 3144 2.21 5 O 3594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19448 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.10, per 1000 atoms: 0.21 Number of scatterers: 19448 At special positions: 0 Unit cell: (122.01, 117.03, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3594 8.00 N 3144 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 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: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 56.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.751A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.130A pdb=" N ASN A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.685A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 770 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.639A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1028 Processing helix chain 'A' and resid 1091 through 1103 Processing helix chain 'A' and resid 1104 through 1123 Processing helix chain 'A' and resid 1132 through 1161 Processing helix chain 'A' and resid 1176 through 1209 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.531A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.715A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 564 through 568 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 617 Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 769 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.588A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1029 Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1091 through 1103 removed outlier: 3.538A pdb=" N SER B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1123 Processing helix chain 'B' and resid 1132 through 1159 Processing helix chain 'B' and resid 1176 through 1209 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.751A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.131A pdb=" N ASN C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.685A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 770 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.639A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1028 Processing helix chain 'C' and resid 1091 through 1103 Processing helix chain 'C' and resid 1104 through 1123 Processing helix chain 'C' and resid 1132 through 1161 Processing helix chain 'C' and resid 1176 through 1209 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.531A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.714A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 617 Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 769 removed outlier: 3.501A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.588A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1029 Processing helix chain 'D' and resid 1039 through 1043 Processing helix chain 'D' and resid 1091 through 1103 removed outlier: 3.538A pdb=" N SER D1103 " --> pdb=" O ALA D1099 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1123 Processing helix chain 'D' and resid 1132 through 1159 Processing helix chain 'D' and resid 1176 through 1209 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 498 removed outlier: 4.833A pdb=" N PHE A 491 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 736 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS A 493 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 734 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.613A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 399 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.631A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.658A pdb=" N VAL B 683 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU B 650 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.658A pdb=" N VAL B 683 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU B 650 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1056 through 1060 Processing sheet with id=AB3, first strand: chain 'B' and resid 1064 through 1066 Processing sheet with id=AB4, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 489 through 498 removed outlier: 4.833A pdb=" N PHE C 491 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR C 736 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS C 493 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE C 734 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 702 through 705 removed outlier: 3.612A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1058 through 1060 Processing sheet with id=AB9, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.630A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 682 through 683 removed outlier: 7.659A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU D 650 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 682 through 683 removed outlier: 7.659A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU D 650 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1056 through 1060 Processing sheet with id=AC6, first strand: chain 'D' and resid 1064 through 1066 1117 hydrogen bonds defined for protein. 3243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5439 1.34 - 1.46: 4181 1.46 - 1.58: 10034 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19882 Sorted by residual: bond pdb=" N THR D1049 " pdb=" CA THR D1049 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 6.99e+00 bond pdb=" N THR B1049 " pdb=" CA THR B1049 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.95e+00 bond pdb=" N LYS D1052 " pdb=" CA LYS D1052 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.15e-02 7.56e+03 5.73e+00 bond pdb=" N LYS B1052 " pdb=" CA LYS B1052 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.63e+00 bond pdb=" N SER B1050 " pdb=" CA SER B1050 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.61e+00 ... (remaining 19877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 26042 2.67 - 5.33: 664 5.33 - 8.00: 136 8.00 - 10.66: 20 10.66 - 13.33: 2 Bond angle restraints: 26864 Sorted by residual: angle pdb=" C ARG A1130 " pdb=" N HIS A1131 " pdb=" CA HIS A1131 " ideal model delta sigma weight residual 121.54 131.98 -10.44 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C ARG C1130 " pdb=" N HIS C1131 " pdb=" CA HIS C1131 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C LYS A1051 " pdb=" N LYS A1052 " pdb=" CA LYS A1052 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C LYS C1051 " pdb=" N LYS C1052 " pdb=" CA LYS C1052 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C GLY D1161 " pdb=" N ASP D1162 " pdb=" CA ASP D1162 " ideal model delta sigma weight residual 123.10 128.13 -5.03 9.60e-01 1.09e+00 2.74e+01 ... (remaining 26859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.08: 11184 20.08 - 40.15: 441 40.15 - 60.23: 67 60.23 - 80.30: 8 80.30 - 100.38: 6 Dihedral angle restraints: 11706 sinusoidal: 4574 harmonic: 7132 Sorted by residual: dihedral pdb=" CA PRO D1083 " pdb=" C PRO D1083 " pdb=" N GLU D1084 " pdb=" CA GLU D1084 " ideal model delta harmonic sigma weight residual 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO B1083 " pdb=" C PRO B1083 " pdb=" N GLU B1084 " pdb=" CA GLU B1084 " ideal model delta harmonic sigma weight residual 180.00 127.11 52.89 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 175.81 -82.81 1 1.00e+01 1.00e-02 8.40e+01 ... (remaining 11703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2619 0.082 - 0.164: 324 0.164 - 0.246: 36 0.246 - 0.328: 13 0.328 - 0.410: 6 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU C1002 " pdb=" CB LEU C1002 " pdb=" CD1 LEU C1002 " pdb=" CD2 LEU C1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CG LEU A1002 " pdb=" CB LEU A1002 " pdb=" CD1 LEU A1002 " pdb=" CD2 LEU A1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2995 not shown) Planarity restraints: 3314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 513 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLY B 513 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY B 513 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 514 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 513 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLY D 513 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY D 513 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL D 514 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 421 " 0.032 2.00e-02 2.50e+03 1.70e-02 5.76e+00 pdb=" CG TYR A 421 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 421 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 421 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 421 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 421 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 421 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 421 " 0.023 2.00e-02 2.50e+03 ... (remaining 3311 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2019 2.75 - 3.29: 20355 3.29 - 3.83: 32550 3.83 - 4.36: 37672 4.36 - 4.90: 63551 Nonbonded interactions: 156147 Sorted by model distance: nonbonded pdb=" O PHE D1106 " pdb=" OG SER D1147 " model vdw 2.214 3.040 nonbonded pdb=" O PHE B1106 " pdb=" OG SER B1147 " model vdw 2.214 3.040 nonbonded pdb=" O PHE C1106 " pdb=" OG SER C1147 " model vdw 2.252 3.040 nonbonded pdb=" O PHE A1106 " pdb=" OG SER A1147 " model vdw 2.253 3.040 nonbonded pdb=" O PRO C1107 " pdb=" OG SER C1110 " model vdw 2.295 3.040 ... (remaining 156142 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19894 Z= 0.299 Angle : 1.077 13.326 26888 Z= 0.588 Chirality : 0.060 0.410 2998 Planarity : 0.006 0.049 3314 Dihedral : 11.182 100.379 7122 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.56 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 4.74 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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 are not related in a simple way. whole: -1.48 (0.14), residues: 2460 helix: -0.43 (0.11), residues: 1318 sheet: -0.85 (0.37), residues: 150 loop : -1.65 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1098 TYR 0.032 0.003 TYR A 421 PHE 0.036 0.003 PHE D1126 TRP 0.023 0.003 TRP B 767 HIS 0.015 0.003 HIS C1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 (19882) covalent geometry : angle 1.07523 / 0.59 (26864) SS BOND : bond 0.00287 / 0.16 ( 12) SS BOND : angle 2.55891 / 1.74 ( 24) hydrogen bonds : bond 0.22957 / 14.94 ( 1109) hydrogen bonds : angle 6.89563 / 4.91 ( 3243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7244 (tt0) cc_final: 0.6741 (tp30) REVERT: A 463 MET cc_start: 0.3776 (ptm) cc_final: 0.3394 (ttm) REVERT: A 474 ILE cc_start: 0.7567 (tt) cc_final: 0.7139 (mp) REVERT: A 478 PRO cc_start: 0.5035 (Cg_endo) cc_final: 0.4806 (Cg_exo) REVERT: A 486 GLU cc_start: 0.8233 (tp30) cc_final: 0.8007 (pt0) REVERT: A 489 ILE cc_start: 0.8138 (pt) cc_final: 0.7765 (pt) REVERT: A 500 ILE cc_start: 0.5864 (mt) cc_final: 0.5190 (mt) REVERT: A 503 MET cc_start: 0.4273 (ttt) cc_final: 0.3855 (ttt) REVERT: A 514 VAL cc_start: 0.8355 (m) cc_final: 0.7906 (m) REVERT: A 527 MET cc_start: 0.7122 (mtt) cc_final: 0.6193 (mpp) REVERT: A 528 CYS cc_start: 0.8896 (m) cc_final: 0.8529 (m) REVERT: A 573 ILE cc_start: 0.8215 (tt) cc_final: 0.8003 (tt) REVERT: A 587 GLN cc_start: 0.6730 (tp40) cc_final: 0.5513 (pt0) REVERT: A 606 TRP cc_start: 0.7270 (m-10) cc_final: 0.6880 (m100) REVERT: A 609 THR cc_start: 0.9303 (m) cc_final: 0.8954 (p) REVERT: A 627 GLU cc_start: 0.3901 (mt-10) cc_final: 0.2861 (pm20) REVERT: A 705 GLU cc_start: 0.5683 (mm-30) cc_final: 0.5415 (mm-30) REVERT: A 721 MET cc_start: 0.5743 (pp-130) cc_final: 0.5223 (mtp) REVERT: A 742 LEU cc_start: 0.5575 (mm) cc_final: 0.5040 (tp) REVERT: A 811 LEU cc_start: 0.8558 (mm) cc_final: 0.8286 (mm) REVERT: A 815 CYS cc_start: 0.7988 (m) cc_final: 0.7637 (p) REVERT: A 1025 ILE cc_start: 0.7984 (mm) cc_final: 0.7712 (tp) REVERT: A 1030 ASP cc_start: 0.7116 (p0) cc_final: 0.6878 (t70) REVERT: A 1059 HIS cc_start: 0.7750 (p-80) cc_final: 0.6472 (p-80) REVERT: A 1169 LYS cc_start: 0.5537 (mtpt) cc_final: 0.5296 (mtmm) REVERT: A 1174 SER cc_start: 0.6190 (p) cc_final: 0.5847 (t) REVERT: A 1191 MET cc_start: 0.7974 (tpp) cc_final: 0.7393 (tpp) REVERT: A 1194 VAL cc_start: 0.7339 (t) cc_final: 0.6975 (t) REVERT: A 1195 LEU cc_start: 0.8345 (mm) cc_final: 0.7986 (mm) outliers start: 6 outliers final: 0 residues processed: 182 average time/residue: 0.0672 time to fit residues: 15.4290 Evaluate side-chains 104 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.122 Evaluate side-chains 193 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7330 (p0) cc_final: 0.6039 (m-40) REVERT: B 414 MET cc_start: 0.8173 (mpt) cc_final: 0.7822 (ptt) REVERT: B 442 LEU cc_start: 0.7839 (mt) cc_final: 0.7246 (mt) REVERT: B 463 MET cc_start: 0.2474 (mtm) cc_final: 0.2046 (mtm) REVERT: B 471 LYS cc_start: 0.6431 (tppp) cc_final: 0.5932 (mttp) REVERT: B 486 GLU cc_start: 0.6890 (tp30) cc_final: 0.6359 (pt0) REVERT: B 511 LYS cc_start: 0.7235 (mmpt) cc_final: 0.6884 (mttm) REVERT: B 519 ASP cc_start: 0.8364 (t70) cc_final: 0.8116 (t0) REVERT: B 527 MET cc_start: 0.8577 (ttp) cc_final: 0.8213 (mmt) REVERT: B 538 VAL cc_start: 0.9070 (t) cc_final: 0.8841 (m) REVERT: B 594 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7519 (ttp-170) REVERT: B 616 TYR cc_start: 0.8441 (t80) cc_final: 0.8164 (t80) REVERT: B 679 PRO cc_start: 0.5498 (Cg_endo) cc_final: 0.4773 (Cg_exo) REVERT: B 688 GLU cc_start: 0.8133 (tt0) cc_final: 0.7719 (tp30) REVERT: B 704 LEU cc_start: 0.7781 (pt) cc_final: 0.7471 (pt) REVERT: B 708 MET cc_start: 0.8289 (tpp) cc_final: 0.7712 (tpp) REVERT: B 710 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7239 (mp0) REVERT: B 713 GLU cc_start: 0.6542 (mt-10) cc_final: 0.5975 (pt0) REVERT: B 714 GLN cc_start: 0.8055 (mm110) cc_final: 0.7620 (mm-40) REVERT: B 720 THR cc_start: 0.5703 (p) cc_final: 0.4743 (p) REVERT: B 752 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8069 (ptpp) REVERT: B 768 TYR cc_start: 0.6598 (m-80) cc_final: 0.6290 (m-10) REVERT: B 769 ASP cc_start: 0.6883 (m-30) cc_final: 0.6515 (t0) REVERT: B 1040 LYS cc_start: 0.4632 (tppt) cc_final: 0.4002 (tppt) REVERT: B 1069 GLU cc_start: 0.6533 (tp30) cc_final: 0.6291 (tp30) REVERT: B 1087 ASP cc_start: 0.5785 (t70) cc_final: 0.5507 (p0) REVERT: B 1116 MET cc_start: 0.8489 (mmt) cc_final: 0.8260 (mmp) REVERT: B 1127 TYR cc_start: 0.5607 (m-10) cc_final: 0.5177 (m-80) REVERT: B 1191 MET cc_start: 0.8608 (mtt) cc_final: 0.8203 (mmm) REVERT: B 1195 LEU cc_start: 0.8827 (mt) cc_final: 0.8614 (mt) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.0636 time to fit residues: 15.5699 Evaluate side-chains 111 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 619 ASN A1081 HIS A1148 ASN A1204 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 726 ASN B 747 ASN B 791 ASN B1081 HIS B1171 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059525 restraints weight = 26589.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061308 restraints weight = 16351.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.062514 restraints weight = 11781.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063259 restraints weight = 9391.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063872 restraints weight = 8067.108| |-----------------------------------------------------------------------------| r_work (final): 0.3246 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.059210 restraints weight = 25078.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060866 restraints weight = 16335.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062051 restraints weight = 12099.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.062776 restraints weight = 9717.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063392 restraints weight = 8397.954| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19894 Z= 0.232 Angle : 0.722 6.881 26888 Z= 0.391 Chirality : 0.043 0.192 2998 Planarity : 0.005 0.064 3314 Dihedral : 6.920 89.146 2694 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.82 % Favored : 95.93 % Rotamer: Outliers : 0.38 % Allowed : 4.79 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 are not related in a simple way. whole: 0.47 (0.16), residues: 2460 helix: 1.58 (0.13), residues: 1342 sheet: -1.03 (0.36), residues: 156 loop : -1.29 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1130 TYR 0.020 0.002 TYR B 647 PHE 0.037 0.003 PHE B 658 TRP 0.014 0.002 TRP D 578 HIS 0.008 0.002 HIS D1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (19882) covalent geometry : angle 0.72071 / 0.39 (26864) SS BOND : bond 0.00355 / 0.23 ( 12) SS BOND : angle 1.74596 / 1.19 ( 24) hydrogen bonds : bond 0.05202 / 3.36 ( 1109) hydrogen bonds : angle 4.75480 / 3.39 ( 3243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 405 TYR cc_start: 0.8431 (m-80) cc_final: 0.7978 (m-80) REVERT: C 406 VAL cc_start: 0.8714 (t) cc_final: 0.8285 (t) REVERT: C 407 MET cc_start: 0.8142 (ttm) cc_final: 0.7822 (mmm) REVERT: C 474 ILE cc_start: 0.8736 (tt) cc_final: 0.8268 (mp) REVERT: C 517 PHE cc_start: 0.8106 (p90) cc_final: 0.7485 (p90) REVERT: C 521 LEU cc_start: 0.8477 (mm) cc_final: 0.8121 (mm) REVERT: C 579 PHE cc_start: 0.9042 (t80) cc_final: 0.8733 (t80) REVERT: C 586 GLN cc_start: 0.7468 (tp40) cc_final: 0.7236 (tp40) REVERT: C 606 TRP cc_start: 0.8084 (m-10) cc_final: 0.7344 (m100) REVERT: C 619 ASN cc_start: 0.7614 (t0) cc_final: 0.6980 (t0) REVERT: C 708 MET cc_start: 0.6675 (tpt) cc_final: 0.6018 (tpt) REVERT: C 727 LEU cc_start: 0.8047 (mm) cc_final: 0.7843 (mm) REVERT: C 1023 MET cc_start: 0.8592 (mmm) cc_final: 0.8343 (mmm) REVERT: C 1036 ARG cc_start: 0.5910 (mmm160) cc_final: 0.5364 (mmm-85) REVERT: C 1057 MET cc_start: 0.7587 (mmm) cc_final: 0.7341 (mmm) REVERT: C 1066 CYS cc_start: 0.2362 (OUTLIER) cc_final: 0.1922 (m) REVERT: C 1147 SER cc_start: 0.8965 (t) cc_final: 0.8626 (p) REVERT: C 1190 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8837 (mm-30) REVERT: C 1191 MET cc_start: 0.7863 (tpp) cc_final: 0.7319 (tpp) REVERT: C 1195 LEU cc_start: 0.8221 (mm) cc_final: 0.7355 (mm) REVERT: C 1301 GLU cc_start: 0.5715 (tp30) cc_final: 0.3932 (tp30) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.0461 time to fit residues: 9.4420 Evaluate side-chains 101 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.132 Evaluate side-chains 131 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6561 (t) cc_final: 0.6265 (p) REVERT: B 408 MET cc_start: 0.6256 (mtt) cc_final: 0.4641 (tmm) REVERT: B 414 MET cc_start: 0.7723 (mpp) cc_final: 0.7364 (ptt) REVERT: B 442 LEU cc_start: 0.7787 (mt) cc_final: 0.7564 (pp) REVERT: B 471 LYS cc_start: 0.6649 (tppp) cc_final: 0.6335 (tttt) REVERT: B 496 MET cc_start: 0.7717 (ttp) cc_final: 0.7404 (ttm) REVERT: B 504 ILE cc_start: 0.7723 (pt) cc_final: 0.7169 (pt) REVERT: B 511 LYS cc_start: 0.7023 (mmpt) cc_final: 0.6522 (mttm) REVERT: B 519 ASP cc_start: 0.8501 (t70) cc_final: 0.8253 (t0) REVERT: B 594 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7440 (ttp-170) REVERT: B 688 GLU cc_start: 0.8130 (tt0) cc_final: 0.7706 (tp30) REVERT: B 704 LEU cc_start: 0.7890 (pt) cc_final: 0.7660 (pt) REVERT: B 708 MET cc_start: 0.7956 (tpp) cc_final: 0.7656 (tpp) REVERT: B 813 GLU cc_start: 0.7051 (tp30) cc_final: 0.6717 (tp30) REVERT: B 1068 LEU cc_start: 0.7373 (pp) cc_final: 0.6770 (pp) REVERT: B 1069 GLU cc_start: 0.6455 (tp30) cc_final: 0.5974 (mp0) REVERT: B 1082 PHE cc_start: 0.7161 (m-80) cc_final: 0.6765 (m-80) REVERT: B 1116 MET cc_start: 0.8356 (mmt) cc_final: 0.8061 (mmp) REVERT: B 1187 ILE cc_start: 0.8724 (mt) cc_final: 0.8391 (mt) REVERT: B 1191 MET cc_start: 0.8570 (mtt) cc_final: 0.8244 (mmm) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.0542 time to fit residues: 9.5179 Evaluate side-chains 83 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 168 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 198 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 128 optimal weight: 0.0570 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN C 619 ASN C1148 ASN C1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061079 restraints weight = 26934.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062963 restraints weight = 16261.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064280 restraints weight = 11636.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065161 restraints weight = 9198.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065658 restraints weight = 7779.498| |-----------------------------------------------------------------------------| r_work (final): 0.3285 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061049 restraints weight = 25589.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062872 restraints weight = 16381.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064202 restraints weight = 11839.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065143 restraints weight = 9276.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.065724 restraints weight = 7780.154| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19894 Z= 0.152 Angle : 0.651 15.257 26888 Z= 0.336 Chirality : 0.041 0.159 2998 Planarity : 0.004 0.061 3314 Dihedral : 6.349 89.697 2694 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.25 % Favored : 96.50 % Rotamer: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: 0.79 (0.17), residues: 2460 helix: 1.96 (0.14), residues: 1324 sheet: -1.42 (0.36), residues: 156 loop : -1.21 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 599 TYR 0.028 0.002 TYR D 647 PHE 0.035 0.002 PHE D 658 TRP 0.023 0.002 TRP D 767 HIS 0.007 0.002 HIS B1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (19882) covalent geometry : angle 0.64731 / 0.33 (26864) SS BOND : bond 0.00636 / 0.41 ( 12) SS BOND : angle 2.52811 / 1.73 ( 24) hydrogen bonds : bond 0.04472 / 2.91 ( 1109) hydrogen bonds : angle 4.34469 / 3.09 ( 3243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8708 (t) cc_final: 0.8215 (t) REVERT: C 407 MET cc_start: 0.8138 (ttm) cc_final: 0.7798 (mmm) REVERT: C 432 ILE cc_start: 0.9101 (pt) cc_final: 0.8883 (mt) REVERT: C 467 LEU cc_start: 0.7660 (mt) cc_final: 0.7448 (mt) REVERT: C 474 ILE cc_start: 0.8682 (tt) cc_final: 0.8219 (mp) REVERT: C 517 PHE cc_start: 0.8033 (p90) cc_final: 0.7365 (p90) REVERT: C 579 PHE cc_start: 0.8971 (t80) cc_final: 0.8687 (t80) REVERT: C 606 TRP cc_start: 0.7872 (m-10) cc_final: 0.7315 (m100) REVERT: C 619 ASN cc_start: 0.7872 (t0) cc_final: 0.7260 (t0) REVERT: C 670 MET cc_start: 0.8241 (mmt) cc_final: 0.7776 (mmp) REVERT: C 1023 MET cc_start: 0.8655 (mmm) cc_final: 0.8318 (mmm) REVERT: C 1068 LEU cc_start: 0.8435 (mt) cc_final: 0.8191 (mt) REVERT: C 1190 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8794 (mm-30) REVERT: C 1191 MET cc_start: 0.7828 (tpp) cc_final: 0.7297 (tpp) REVERT: C 1195 LEU cc_start: 0.8168 (mm) cc_final: 0.7341 (mm) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.0523 time to fit residues: 9.9801 Evaluate side-chains 101 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.179 Evaluate side-chains 120 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6422 (t) cc_final: 0.6134 (p) REVERT: B 408 MET cc_start: 0.6126 (mtt) cc_final: 0.4376 (tmm) REVERT: B 414 MET cc_start: 0.7743 (mpp) cc_final: 0.7386 (ptt) REVERT: B 496 MET cc_start: 0.7577 (ttp) cc_final: 0.7304 (ttm) REVERT: B 504 ILE cc_start: 0.7576 (pt) cc_final: 0.7096 (pt) REVERT: B 511 LYS cc_start: 0.6977 (mmpt) cc_final: 0.6478 (mttm) REVERT: B 519 ASP cc_start: 0.8357 (t70) cc_final: 0.8094 (t0) REVERT: B 521 LEU cc_start: 0.8363 (mp) cc_final: 0.8124 (mp) REVERT: B 594 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.7371 (ttp-170) REVERT: B 688 GLU cc_start: 0.8179 (tt0) cc_final: 0.7598 (tp30) REVERT: B 704 LEU cc_start: 0.7972 (pt) cc_final: 0.7752 (pp) REVERT: B 1068 LEU cc_start: 0.7432 (pp) cc_final: 0.6783 (pp) REVERT: B 1069 GLU cc_start: 0.6473 (tp30) cc_final: 0.5980 (mp0) REVERT: B 1187 ILE cc_start: 0.8735 (mt) cc_final: 0.8390 (mt) REVERT: B 1191 MET cc_start: 0.8631 (mtt) cc_final: 0.8275 (mmm) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0531 time to fit residues: 8.6598 Evaluate side-chains 81 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 175 optimal weight: 0.0970 chunk 235 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.078614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060335 restraints weight = 27653.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062113 restraints weight = 17068.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063382 restraints weight = 12309.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064240 restraints weight = 9775.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064760 restraints weight = 8299.597| |-----------------------------------------------------------------------------| r_work (final): 0.3250 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059788 restraints weight = 25359.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061583 restraints weight = 16385.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062803 restraints weight = 11893.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063680 restraints weight = 9424.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064083 restraints weight = 7945.231| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19894 Z= 0.168 Angle : 0.634 10.533 26888 Z= 0.334 Chirality : 0.041 0.192 2998 Planarity : 0.004 0.035 3314 Dihedral : 6.182 88.208 2694 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: 0.84 (0.17), residues: 2460 helix: 2.03 (0.14), residues: 1322 sheet: -1.51 (0.35), residues: 160 loop : -1.17 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 599 TYR 0.019 0.002 TYR C 440 PHE 0.029 0.002 PHE D 658 TRP 0.021 0.002 TRP A1032 HIS 0.007 0.001 HIS D1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (19882) covalent geometry : angle 0.63097 / 0.33 (26864) SS BOND : bond 0.00964 / 0.61 ( 12) SS BOND : angle 2.15989 / 1.53 ( 24) hydrogen bonds : bond 0.04244 / 2.77 ( 1109) hydrogen bonds : angle 4.37102 / 3.11 ( 3243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8731 (t) cc_final: 0.8158 (t) REVERT: C 407 MET cc_start: 0.8101 (ttm) cc_final: 0.7714 (mmm) REVERT: C 442 LEU cc_start: 0.8688 (mm) cc_final: 0.8167 (tp) REVERT: C 474 ILE cc_start: 0.8681 (tt) cc_final: 0.8227 (mp) REVERT: C 517 PHE cc_start: 0.8118 (p90) cc_final: 0.7380 (p90) REVERT: C 606 TRP cc_start: 0.7914 (m-10) cc_final: 0.7312 (m100) REVERT: C 619 ASN cc_start: 0.7609 (t0) cc_final: 0.7342 (t0) REVERT: C 670 MET cc_start: 0.8278 (mmt) cc_final: 0.7689 (mmp) REVERT: C 674 MET cc_start: 0.6659 (mtm) cc_final: 0.6128 (mtm) REVERT: C 708 MET cc_start: 0.6080 (tpt) cc_final: 0.5857 (tpt) REVERT: C 1023 MET cc_start: 0.8712 (mmm) cc_final: 0.8469 (mmm) REVERT: C 1068 LEU cc_start: 0.8440 (mt) cc_final: 0.8224 (mt) REVERT: C 1190 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8823 (mm-30) REVERT: C 1191 MET cc_start: 0.7886 (tpp) cc_final: 0.7350 (tpp) REVERT: C 1195 LEU cc_start: 0.8147 (mm) cc_final: 0.7388 (mm) REVERT: C 1301 GLU cc_start: 0.6585 (tp30) cc_final: 0.5411 (tp30) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.0482 time to fit residues: 8.4114 Evaluate side-chains 96 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.110 Evaluate side-chains 110 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6461 (t) cc_final: 0.6176 (p) REVERT: B 408 MET cc_start: 0.6172 (mtt) cc_final: 0.4383 (tmm) REVERT: B 414 MET cc_start: 0.7737 (mpp) cc_final: 0.7409 (ptt) REVERT: B 463 MET cc_start: 0.4843 (mmm) cc_final: 0.4606 (mmt) REVERT: B 496 MET cc_start: 0.7651 (ttp) cc_final: 0.7343 (ttm) REVERT: B 504 ILE cc_start: 0.7572 (pt) cc_final: 0.7291 (pt) REVERT: B 511 LYS cc_start: 0.6928 (mmpt) cc_final: 0.6438 (mttt) REVERT: B 519 ASP cc_start: 0.8392 (t70) cc_final: 0.8134 (t0) REVERT: B 521 LEU cc_start: 0.8291 (mp) cc_final: 0.8086 (mp) REVERT: B 594 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7526 (ttp-170) REVERT: B 688 GLU cc_start: 0.8173 (tt0) cc_final: 0.7595 (tp30) REVERT: B 813 GLU cc_start: 0.7221 (tp30) cc_final: 0.6880 (tp30) REVERT: B 1068 LEU cc_start: 0.7507 (pp) cc_final: 0.6900 (pp) REVERT: B 1069 GLU cc_start: 0.6495 (tp30) cc_final: 0.6045 (mp0) REVERT: B 1187 ILE cc_start: 0.8631 (mt) cc_final: 0.8284 (mt) REVERT: B 1191 MET cc_start: 0.8692 (mtt) cc_final: 0.8307 (mmm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0520 time to fit residues: 7.8959 Evaluate side-chains 80 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 83 optimal weight: 0.0050 chunk 239 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 175 optimal weight: 0.0980 chunk 41 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN C1204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.079719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061448 restraints weight = 27486.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063311 restraints weight = 17040.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064611 restraints weight = 12185.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065485 restraints weight = 9652.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065974 restraints weight = 8187.004| |-----------------------------------------------------------------------------| r_work (final): 0.3277 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060287 restraints weight = 25320.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062087 restraints weight = 16311.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063405 restraints weight = 11923.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064208 restraints weight = 9537.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064896 restraints weight = 8197.348| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19894 Z= 0.131 Angle : 0.618 13.329 26888 Z= 0.319 Chirality : 0.041 0.147 2998 Planarity : 0.005 0.124 3314 Dihedral : 5.987 87.969 2694 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: 0.82 (0.17), residues: 2460 helix: 1.97 (0.14), residues: 1336 sheet: -1.25 (0.36), residues: 156 loop : -1.22 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 599 TYR 0.024 0.002 TYR B 647 PHE 0.024 0.002 PHE B 658 TRP 0.019 0.002 TRP C1063 HIS 0.008 0.001 HIS C1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19882) covalent geometry : angle 0.61459 / 0.32 (26864) SS BOND : bond 0.00507 / 0.32 ( 12) SS BOND : angle 2.22849 / 1.58 ( 24) hydrogen bonds : bond 0.03927 / 2.58 ( 1109) hydrogen bonds : angle 4.26057 / 3.01 ( 3243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8647 (t) cc_final: 0.8084 (t) REVERT: C 407 MET cc_start: 0.8040 (ttm) cc_final: 0.7667 (mmm) REVERT: C 434 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7308 (mmtp) REVERT: C 442 LEU cc_start: 0.8581 (mm) cc_final: 0.8091 (tp) REVERT: C 474 ILE cc_start: 0.8659 (tt) cc_final: 0.8216 (mp) REVERT: C 517 PHE cc_start: 0.8074 (p90) cc_final: 0.7270 (p90) REVERT: C 599 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6859 (mmm160) REVERT: C 606 TRP cc_start: 0.7952 (m-10) cc_final: 0.7465 (m100) REVERT: C 670 MET cc_start: 0.8203 (mmt) cc_final: 0.7650 (mmp) REVERT: C 673 TYR cc_start: 0.6971 (m-10) cc_final: 0.6734 (m-10) REVERT: C 674 MET cc_start: 0.6763 (mtm) cc_final: 0.6500 (mtp) REVERT: C 708 MET cc_start: 0.6137 (tpt) cc_final: 0.5479 (tpt) REVERT: C 1023 MET cc_start: 0.8698 (mmm) cc_final: 0.8482 (mmm) REVERT: C 1097 LEU cc_start: 0.8670 (pp) cc_final: 0.8449 (pp) REVERT: C 1180 TYR cc_start: 0.8581 (m-80) cc_final: 0.8262 (m-80) REVERT: C 1190 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8881 (mt-10) REVERT: C 1191 MET cc_start: 0.7812 (tpp) cc_final: 0.7279 (tpp) REVERT: C 1195 LEU cc_start: 0.8160 (mm) cc_final: 0.7336 (mm) REVERT: C 1200 PHE cc_start: 0.8284 (t80) cc_final: 0.8077 (t80) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.0558 time to fit residues: 9.9003 Evaluate side-chains 92 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.184 Evaluate side-chains 122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6564 (t) cc_final: 0.6251 (p) REVERT: B 408 MET cc_start: 0.6114 (mtt) cc_final: 0.4340 (tmm) REVERT: B 414 MET cc_start: 0.7737 (mpp) cc_final: 0.7391 (ptt) REVERT: B 463 MET cc_start: 0.4704 (mmm) cc_final: 0.4498 (mmt) REVERT: B 496 MET cc_start: 0.7582 (ttp) cc_final: 0.7253 (ttm) REVERT: B 503 MET cc_start: 0.8409 (ttp) cc_final: 0.8110 (tmm) REVERT: B 504 ILE cc_start: 0.7571 (pt) cc_final: 0.7355 (pt) REVERT: B 511 LYS cc_start: 0.6847 (mmpt) cc_final: 0.6396 (mttt) REVERT: B 519 ASP cc_start: 0.8304 (t70) cc_final: 0.8056 (t0) REVERT: B 521 LEU cc_start: 0.8476 (mp) cc_final: 0.8267 (mp) REVERT: B 594 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7524 (ttp-170) REVERT: B 688 GLU cc_start: 0.8156 (tt0) cc_final: 0.7541 (tp30) REVERT: B 813 GLU cc_start: 0.7202 (tp30) cc_final: 0.6762 (tp30) REVERT: B 1068 LEU cc_start: 0.7505 (pp) cc_final: 0.6912 (pp) REVERT: B 1069 GLU cc_start: 0.6393 (tp30) cc_final: 0.5960 (mp0) REVERT: B 1141 PHE cc_start: 0.8313 (m-80) cc_final: 0.7671 (m-80) REVERT: B 1187 ILE cc_start: 0.8684 (mt) cc_final: 0.8338 (mt) REVERT: B 1191 MET cc_start: 0.8729 (mtt) cc_final: 0.8322 (mmm) REVERT: B 1198 HIS cc_start: 0.8649 (m-70) cc_final: 0.8305 (t70) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.0497 time to fit residues: 8.3751 Evaluate side-chains 86 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 149 optimal weight: 10.0000 chunk 56 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN C 619 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.080683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.062597 restraints weight = 26147.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064312 restraints weight = 16564.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.065556 restraints weight = 12133.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066435 restraints weight = 9655.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067059 restraints weight = 8210.025| |-----------------------------------------------------------------------------| r_work (final): 0.3316 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.079166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061173 restraints weight = 25994.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063127 restraints weight = 16490.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064476 restraints weight = 11855.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065370 restraints weight = 9314.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066035 restraints weight = 7877.393| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19894 Z= 0.125 Angle : 0.606 9.123 26888 Z= 0.310 Chirality : 0.041 0.183 2998 Planarity : 0.004 0.080 3314 Dihedral : 5.839 91.763 2694 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: 0.86 (0.17), residues: 2460 helix: 1.98 (0.14), residues: 1326 sheet: -1.05 (0.38), residues: 136 loop : -1.18 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 715 TYR 0.016 0.001 TYR C 440 PHE 0.026 0.002 PHE C1140 TRP 0.023 0.001 TRP C1063 HIS 0.007 0.001 HIS D1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (19882) covalent geometry : angle 0.60302 / 0.31 (26864) SS BOND : bond 0.00678 / 0.47 ( 12) SS BOND : angle 2.25432 / 1.58 ( 24) hydrogen bonds : bond 0.03703 / 2.42 ( 1109) hydrogen bonds : angle 4.15699 / 2.96 ( 3243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8768 (t) cc_final: 0.8198 (t) REVERT: C 407 MET cc_start: 0.8098 (ttm) cc_final: 0.7727 (mmm) REVERT: C 434 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7318 (mmtp) REVERT: C 442 LEU cc_start: 0.8623 (mm) cc_final: 0.8002 (tp) REVERT: C 474 ILE cc_start: 0.8696 (tt) cc_final: 0.8298 (mp) REVERT: C 517 PHE cc_start: 0.7880 (p90) cc_final: 0.7471 (p90) REVERT: C 599 ARG cc_start: 0.7412 (mmm160) cc_final: 0.6723 (mmm160) REVERT: C 606 TRP cc_start: 0.8061 (m-10) cc_final: 0.7486 (m100) REVERT: C 670 MET cc_start: 0.8329 (mmt) cc_final: 0.7697 (mmp) REVERT: C 673 TYR cc_start: 0.6940 (m-10) cc_final: 0.6718 (m-80) REVERT: C 708 MET cc_start: 0.6207 (tpt) cc_final: 0.5966 (tpt) REVERT: C 1057 MET cc_start: 0.8170 (mmm) cc_final: 0.7955 (mmm) REVERT: C 1069 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6340 (tp30) REVERT: C 1097 LEU cc_start: 0.8687 (pp) cc_final: 0.8480 (pp) REVERT: C 1190 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8929 (mt-10) REVERT: C 1191 MET cc_start: 0.7758 (tpp) cc_final: 0.7441 (tpp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0554 time to fit residues: 10.2247 Evaluate side-chains 94 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.111 Evaluate side-chains 116 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.6071 (mtt) cc_final: 0.4269 (tmm) REVERT: B 414 MET cc_start: 0.7710 (mpp) cc_final: 0.7389 (ptt) REVERT: B 496 MET cc_start: 0.7468 (ttp) cc_final: 0.7135 (ttm) REVERT: B 503 MET cc_start: 0.8391 (ttp) cc_final: 0.8069 (tmm) REVERT: B 504 ILE cc_start: 0.7563 (pt) cc_final: 0.7161 (pt) REVERT: B 511 LYS cc_start: 0.6621 (mmpt) cc_final: 0.6226 (mttt) REVERT: B 519 ASP cc_start: 0.8297 (t70) cc_final: 0.7994 (t0) REVERT: B 527 MET cc_start: 0.8070 (ptp) cc_final: 0.7290 (mtp) REVERT: B 594 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7511 (ttp-170) REVERT: B 688 GLU cc_start: 0.8128 (tt0) cc_final: 0.7380 (tp30) REVERT: B 702 TYR cc_start: 0.5552 (t80) cc_final: 0.4780 (t80) REVERT: B 704 LEU cc_start: 0.7695 (pp) cc_final: 0.7442 (mt) REVERT: B 798 ILE cc_start: 0.8724 (mt) cc_final: 0.8471 (mm) REVERT: B 813 GLU cc_start: 0.7164 (tp30) cc_final: 0.6794 (tp30) REVERT: B 1023 MET cc_start: 0.8664 (mmm) cc_final: 0.8306 (mmm) REVERT: B 1068 LEU cc_start: 0.7481 (pp) cc_final: 0.6798 (pp) REVERT: B 1069 GLU cc_start: 0.6475 (tp30) cc_final: 0.5994 (mp0) REVERT: B 1080 ASP cc_start: 0.7373 (t70) cc_final: 0.7002 (t0) REVERT: B 1141 PHE cc_start: 0.8289 (m-80) cc_final: 0.7671 (m-80) REVERT: B 1170 LYS cc_start: 0.6293 (mmmt) cc_final: 0.5729 (tmtt) REVERT: B 1187 ILE cc_start: 0.8712 (mt) cc_final: 0.8374 (mt) REVERT: B 1191 MET cc_start: 0.8714 (mtt) cc_final: 0.8340 (mmm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0496 time to fit residues: 7.9456 Evaluate side-chains 85 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 30 optimal weight: 0.0770 chunk 156 optimal weight: 10.0000 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN B1008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.081368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.063194 restraints weight = 26650.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.065019 restraints weight = 16630.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.066316 restraints weight = 11970.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.067211 restraints weight = 9459.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.067794 restraints weight = 8042.469| |-----------------------------------------------------------------------------| r_work (final): 0.3329 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062110 restraints weight = 25119.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.063838 restraints weight = 16951.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065067 restraints weight = 12615.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065995 restraints weight = 10124.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066498 restraints weight = 8539.185| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19894 Z= 0.122 Angle : 0.633 17.809 26888 Z= 0.315 Chirality : 0.042 0.356 2998 Planarity : 0.004 0.061 3314 Dihedral : 5.714 92.016 2694 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 are not related in a simple way. whole: 0.84 (0.17), residues: 2460 helix: 1.87 (0.14), residues: 1342 sheet: -0.26 (0.46), residues: 104 loop : -1.20 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 594 TYR 0.016 0.001 TYR A 421 PHE 0.024 0.002 PHE C 579 TRP 0.023 0.001 TRP A1063 HIS 0.007 0.001 HIS D1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19882) covalent geometry : angle 0.62941 / 0.31 (26864) SS BOND : bond 0.00156 / 0.12 ( 12) SS BOND : angle 2.18276 / 1.53 ( 24) hydrogen bonds : bond 0.03603 / 2.36 ( 1109) hydrogen bonds : angle 4.10869 / 2.92 ( 3243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.181 Fit side-chains REVERT: C 406 VAL cc_start: 0.8811 (t) cc_final: 0.8180 (t) REVERT: C 407 MET cc_start: 0.8144 (ttm) cc_final: 0.7733 (mmm) REVERT: C 434 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7255 (mmtp) REVERT: C 442 LEU cc_start: 0.8660 (mm) cc_final: 0.8041 (tp) REVERT: C 474 ILE cc_start: 0.8690 (tt) cc_final: 0.8276 (mp) REVERT: C 496 MET cc_start: 0.6618 (ppp) cc_final: 0.6364 (ppp) REVERT: C 517 PHE cc_start: 0.7825 (p90) cc_final: 0.7277 (p90) REVERT: C 581 LEU cc_start: 0.8258 (mm) cc_final: 0.8053 (mm) REVERT: C 599 ARG cc_start: 0.7472 (mmm160) cc_final: 0.6730 (mmm160) REVERT: C 606 TRP cc_start: 0.8053 (m-10) cc_final: 0.7481 (m100) REVERT: C 670 MET cc_start: 0.8379 (mmt) cc_final: 0.7754 (mmp) REVERT: C 708 MET cc_start: 0.6173 (tpt) cc_final: 0.5885 (tpt) REVERT: C 803 LEU cc_start: 0.8842 (mt) cc_final: 0.8546 (pp) REVERT: C 1025 ILE cc_start: 0.8228 (mm) cc_final: 0.7995 (pt) REVERT: C 1069 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6217 (tp30) REVERT: C 1190 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8954 (mt-10) REVERT: C 1191 MET cc_start: 0.7697 (tpp) cc_final: 0.7397 (tpp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0541 time to fit residues: 9.4997 Evaluate side-chains 95 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.183 Evaluate side-chains 122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.6044 (mtt) cc_final: 0.4165 (tmm) REVERT: B 414 MET cc_start: 0.7708 (mpp) cc_final: 0.7368 (ptt) REVERT: B 496 MET cc_start: 0.7389 (ttp) cc_final: 0.7085 (ttm) REVERT: B 503 MET cc_start: 0.8332 (ttp) cc_final: 0.8053 (tmm) REVERT: B 504 ILE cc_start: 0.7606 (pt) cc_final: 0.7200 (pt) REVERT: B 511 LYS cc_start: 0.6566 (mmpt) cc_final: 0.6250 (mttt) REVERT: B 519 ASP cc_start: 0.8334 (t70) cc_final: 0.7953 (t0) REVERT: B 527 MET cc_start: 0.7897 (ptp) cc_final: 0.7089 (mtp) REVERT: B 570 GLU cc_start: 0.6749 (tp30) cc_final: 0.6349 (mm-30) REVERT: B 581 LEU cc_start: 0.9124 (tt) cc_final: 0.8915 (tp) REVERT: B 594 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7445 (ttp-170) REVERT: B 688 GLU cc_start: 0.8087 (tt0) cc_final: 0.7284 (tp30) REVERT: B 702 TYR cc_start: 0.5497 (t80) cc_final: 0.4968 (t80) REVERT: B 704 LEU cc_start: 0.7790 (pp) cc_final: 0.7533 (mt) REVERT: B 713 GLU cc_start: 0.7592 (tp30) cc_final: 0.6507 (pt0) REVERT: B 720 THR cc_start: 0.7197 (p) cc_final: 0.6069 (p) REVERT: B 798 ILE cc_start: 0.8614 (mt) cc_final: 0.8355 (mm) REVERT: B 813 GLU cc_start: 0.7183 (tp30) cc_final: 0.6781 (tp30) REVERT: B 1068 LEU cc_start: 0.7468 (pp) cc_final: 0.6779 (pp) REVERT: B 1069 GLU cc_start: 0.6484 (tp30) cc_final: 0.6010 (mp0) REVERT: B 1141 PHE cc_start: 0.8256 (m-80) cc_final: 0.7657 (m-80) REVERT: B 1170 LYS cc_start: 0.6278 (mmmt) cc_final: 0.5741 (tmtt) REVERT: B 1187 ILE cc_start: 0.8744 (mt) cc_final: 0.8398 (mt) REVERT: B 1191 MET cc_start: 0.8724 (mtt) cc_final: 0.8357 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0532 time to fit residues: 8.8257 Evaluate side-chains 88 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 66 optimal weight: 0.0970 chunk 198 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN C 575 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.079547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.061873 restraints weight = 27134.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.063653 restraints weight = 16783.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.064914 restraints weight = 12145.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065795 restraints weight = 9602.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066372 restraints weight = 8115.627| |-----------------------------------------------------------------------------| r_work (final): 0.3304 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060162 restraints weight = 25728.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061893 restraints weight = 16839.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063134 restraints weight = 12399.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063712 restraints weight = 9870.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064500 restraints weight = 8605.132| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19894 Z= 0.161 Angle : 0.652 15.630 26888 Z= 0.333 Chirality : 0.043 0.496 2998 Planarity : 0.004 0.048 3314 Dihedral : 5.769 92.386 2694 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 are not related in a simple way. whole: 0.79 (0.17), residues: 2460 helix: 1.82 (0.14), residues: 1352 sheet: -0.40 (0.44), residues: 120 loop : -1.24 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1036 TYR 0.018 0.002 TYR D 702 PHE 0.021 0.002 PHE D 607 TRP 0.019 0.002 TRP C1063 HIS 0.006 0.001 HIS D1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (19882) covalent geometry : angle 0.64933 / 0.33 (26864) SS BOND : bond 0.00237 / 0.15 ( 12) SS BOND : angle 2.13862 / 1.51 ( 24) hydrogen bonds : bond 0.03696 / 2.42 ( 1109) hydrogen bonds : angle 4.25314 / 3.02 ( 3243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8744 (t) cc_final: 0.8154 (t) REVERT: C 407 MET cc_start: 0.8173 (ttm) cc_final: 0.7774 (mmm) REVERT: C 434 LYS cc_start: 0.7599 (mtmm) cc_final: 0.7340 (mmtp) REVERT: C 442 LEU cc_start: 0.8700 (mm) cc_final: 0.8112 (tp) REVERT: C 581 LEU cc_start: 0.8270 (mm) cc_final: 0.7956 (mm) REVERT: C 606 TRP cc_start: 0.8105 (m-10) cc_final: 0.7512 (m100) REVERT: C 670 MET cc_start: 0.8395 (mmt) cc_final: 0.7784 (mmp) REVERT: C 708 MET cc_start: 0.6177 (tpt) cc_final: 0.5935 (tpt) REVERT: C 1023 MET cc_start: 0.8605 (mmm) cc_final: 0.8358 (mmm) REVERT: C 1069 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6262 (tp30) REVERT: C 1190 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8939 (mt-10) REVERT: C 1191 MET cc_start: 0.7736 (tpp) cc_final: 0.7438 (tpp) REVERT: C 1301 GLU cc_start: 0.6365 (tp30) cc_final: 0.5050 (tp30) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0508 time to fit residues: 8.7539 Evaluate side-chains 86 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.183 Evaluate side-chains 106 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: B 408 MET cc_start: 0.6011 (mtt) cc_final: 0.3932 (tmm) REVERT: B 414 MET cc_start: 0.7732 (mpp) cc_final: 0.7380 (ptt) REVERT: B 503 MET cc_start: 0.8337 (ttp) cc_final: 0.8032 (tmm) REVERT: B 504 ILE cc_start: 0.7524 (pt) cc_final: 0.7028 (pt) REVERT: B 519 ASP cc_start: 0.8218 (t70) cc_final: 0.7971 (t0) REVERT: B 527 MET cc_start: 0.7791 (ptp) cc_final: 0.7051 (mtp) REVERT: B 570 GLU cc_start: 0.7061 (tp30) cc_final: 0.6810 (mm-30) REVERT: B 573 ILE cc_start: 0.7944 (pt) cc_final: 0.7706 (pt) REVERT: B 594 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7538 (ttp-170) REVERT: B 607 PHE cc_start: 0.8444 (t80) cc_final: 0.8162 (t80) REVERT: B 688 GLU cc_start: 0.8110 (tt0) cc_final: 0.7458 (tp30) REVERT: B 1023 MET cc_start: 0.8685 (mmm) cc_final: 0.8399 (mmm) REVERT: B 1141 PHE cc_start: 0.8272 (m-80) cc_final: 0.7628 (m-80) REVERT: B 1187 ILE cc_start: 0.8717 (mt) cc_final: 0.8371 (mt) REVERT: B 1191 MET cc_start: 0.8758 (mtt) cc_final: 0.8330 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0480 time to fit residues: 7.2672 Evaluate side-chains 82 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 25 optimal weight: 0.5980 chunk 208 optimal weight: 0.0030 chunk 237 optimal weight: 6.9990 chunk 111 optimal weight: 0.0670 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 5 optimal weight: 0.0370 chunk 117 optimal weight: 3.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN B1008 GLN C1132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.081803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.063876 restraints weight = 26579.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065676 restraints weight = 16743.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.066980 restraints weight = 12115.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.067894 restraints weight = 9576.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068510 restraints weight = 8068.667| |-----------------------------------------------------------------------------| r_work (final): 0.3344 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062319 restraints weight = 25144.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.064135 restraints weight = 16470.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.065381 restraints weight = 12046.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066162 restraints weight = 9596.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066883 restraints weight = 8186.092| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19894 Z= 0.124 Angle : 0.651 17.487 26888 Z= 0.326 Chirality : 0.043 0.419 2998 Planarity : 0.003 0.040 3314 Dihedral : 5.720 92.019 2694 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 are not related in a simple way. whole: 0.88 (0.17), residues: 2460 helix: 1.87 (0.14), residues: 1340 sheet: 0.01 (0.47), residues: 120 loop : -1.18 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 675 TYR 0.018 0.001 TYR B 647 PHE 0.022 0.002 PHE A 579 TRP 0.026 0.002 TRP D 605 HIS 0.007 0.001 HIS D1081 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (19882) covalent geometry : angle 0.64454 / 0.32 (26864) SS BOND : bond 0.00206 / 0.14 ( 12) SS BOND : angle 3.09672 / 2.20 ( 24) hydrogen bonds : bond 0.03580 / 2.35 ( 1109) hydrogen bonds : angle 4.15153 / 2.94 ( 3243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8697 (t) cc_final: 0.8133 (t) REVERT: C 407 MET cc_start: 0.8126 (ttm) cc_final: 0.7748 (mmm) REVERT: C 434 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7224 (mmtp) REVERT: C 517 PHE cc_start: 0.8014 (p90) cc_final: 0.7719 (p90) REVERT: C 534 ILE cc_start: 0.8865 (mm) cc_final: 0.8662 (mm) REVERT: C 581 LEU cc_start: 0.8227 (mm) cc_final: 0.7935 (mm) REVERT: C 606 TRP cc_start: 0.8034 (m-10) cc_final: 0.7712 (m100) REVERT: C 670 MET cc_start: 0.8256 (mmt) cc_final: 0.7745 (mmt) REVERT: C 671 TRP cc_start: 0.7308 (t-100) cc_final: 0.6956 (t-100) REVERT: C 673 TYR cc_start: 0.6736 (m-80) cc_final: 0.6298 (t80) REVERT: C 708 MET cc_start: 0.6146 (tpt) cc_final: 0.5899 (tpt) REVERT: C 803 LEU cc_start: 0.8862 (mt) cc_final: 0.8552 (pp) REVERT: C 1057 MET cc_start: 0.8405 (mmm) cc_final: 0.8153 (mmm) REVERT: C 1068 LEU cc_start: 0.8432 (mt) cc_final: 0.8225 (mt) REVERT: C 1069 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6204 (tp30) REVERT: C 1190 GLU cc_start: 0.9378 (mm-30) cc_final: 0.8931 (mt-10) REVERT: C 1191 MET cc_start: 0.7721 (tpp) cc_final: 0.7393 (tpp) REVERT: C 1301 GLU cc_start: 0.5492 (tp30) cc_final: 0.5224 (tp30) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0484 time to fit residues: 8.2942 Evaluate side-chains 91 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.181 Evaluate side-chains 106 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 408 MET cc_start: 0.6055 (mtt) cc_final: 0.4005 (tmm) REVERT: B 496 MET cc_start: 0.7611 (ttp) cc_final: 0.7384 (ttm) REVERT: B 503 MET cc_start: 0.8339 (ttp) cc_final: 0.8089 (tmm) REVERT: B 504 ILE cc_start: 0.7510 (pt) cc_final: 0.7121 (pt) REVERT: B 527 MET cc_start: 0.7849 (ptp) cc_final: 0.7135 (mtp) REVERT: B 570 GLU cc_start: 0.7019 (tp30) cc_final: 0.6773 (mm-30) REVERT: B 594 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7514 (ttp-170) REVERT: B 688 GLU cc_start: 0.8036 (tt0) cc_final: 0.7294 (tp30) REVERT: B 713 GLU cc_start: 0.7617 (tp30) cc_final: 0.6504 (pt0) REVERT: B 720 THR cc_start: 0.7258 (p) cc_final: 0.6187 (p) REVERT: B 798 ILE cc_start: 0.8645 (mt) cc_final: 0.8383 (mm) REVERT: B 1023 MET cc_start: 0.8687 (mmm) cc_final: 0.8126 (mmm) REVERT: B 1141 PHE cc_start: 0.8270 (m-80) cc_final: 0.7646 (m-80) REVERT: B 1170 LYS cc_start: 0.6286 (mmmt) cc_final: 0.5753 (tmtt) REVERT: B 1187 ILE cc_start: 0.8736 (mt) cc_final: 0.8395 (mt) REVERT: B 1191 MET cc_start: 0.8747 (mtt) cc_final: 0.8311 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0459 time to fit residues: 6.9305 Evaluate side-chains 82 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 124 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 233 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN B1008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.079486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061630 restraints weight = 27747.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.063462 restraints weight = 17518.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.064585 restraints weight = 12660.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.065536 restraints weight = 10269.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.066153 restraints weight = 8648.460| |-----------------------------------------------------------------------------| r_work (final): 0.3292 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059913 restraints weight = 24998.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061687 restraints weight = 16258.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062968 restraints weight = 11881.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.063707 restraints weight = 9364.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064435 restraints weight = 7999.538| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19894 Z= 0.166 Angle : 0.693 17.143 26888 Z= 0.349 Chirality : 0.044 0.479 2998 Planarity : 0.004 0.046 3314 Dihedral : 5.856 92.453 2694 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 are not related in a simple way. whole: 0.74 (0.17), residues: 2460 helix: 1.73 (0.14), residues: 1346 sheet: -0.15 (0.47), residues: 120 loop : -1.20 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 675 TYR 0.019 0.002 TYR B 702 PHE 0.021 0.002 PHE D 607 TRP 0.018 0.002 TRP C 460 HIS 0.006 0.002 HIS D1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (19882) covalent geometry : angle 0.68751 / 0.35 (26864) SS BOND : bond 0.00313 / 0.20 ( 12) SS BOND : angle 2.92378 / 2.07 ( 24) hydrogen bonds : bond 0.03660 / 2.40 ( 1109) hydrogen bonds : angle 4.36934 / 3.09 ( 3243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: C 406 VAL cc_start: 0.8637 (t) cc_final: 0.8314 (t) REVERT: C 434 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7201 (mmtp) REVERT: C 517 PHE cc_start: 0.7997 (p90) cc_final: 0.7715 (p90) REVERT: C 534 ILE cc_start: 0.8904 (mm) cc_final: 0.8588 (mm) REVERT: C 581 LEU cc_start: 0.8291 (mm) cc_final: 0.7973 (mm) REVERT: C 606 TRP cc_start: 0.8111 (m-10) cc_final: 0.7570 (m100) REVERT: C 670 MET cc_start: 0.8277 (mmt) cc_final: 0.7938 (mmp) REVERT: C 673 TYR cc_start: 0.6443 (m-80) cc_final: 0.6033 (t80) REVERT: C 708 MET cc_start: 0.6151 (tpt) cc_final: 0.5731 (tpp) REVERT: C 751 LEU cc_start: 0.8093 (mt) cc_final: 0.7838 (tt) REVERT: C 1023 MET cc_start: 0.8722 (mmp) cc_final: 0.8453 (mmm) REVERT: C 1057 MET cc_start: 0.8372 (mmm) cc_final: 0.8128 (mmm) REVERT: C 1069 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6251 (tp30) REVERT: C 1113 LEU cc_start: 0.8865 (mt) cc_final: 0.8607 (tp) REVERT: C 1190 GLU cc_start: 0.9379 (mm-30) cc_final: 0.8901 (mm-30) REVERT: C 1191 MET cc_start: 0.7762 (tpp) cc_final: 0.7486 (tpp) REVERT: C 1301 GLU cc_start: 0.6087 (tp30) cc_final: 0.5154 (tp30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0537 time to fit residues: 8.6496 Evaluate side-chains 81 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.193 Evaluate side-chains 100 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.163 Fit side-chains REVERT: B 408 MET cc_start: 0.6009 (mtt) cc_final: 0.3878 (tmm) REVERT: B 414 MET cc_start: 0.7717 (mtt) cc_final: 0.7462 (ptt) REVERT: B 496 MET cc_start: 0.7585 (ttp) cc_final: 0.7363 (ttm) REVERT: B 503 MET cc_start: 0.8339 (ttp) cc_final: 0.8038 (tmm) REVERT: B 527 MET cc_start: 0.7904 (ptp) cc_final: 0.7125 (mtp) REVERT: B 594 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7588 (ttp-170) REVERT: B 607 PHE cc_start: 0.8470 (t80) cc_final: 0.8207 (t80) REVERT: B 688 GLU cc_start: 0.8093 (tt0) cc_final: 0.7425 (tp30) REVERT: B 1023 MET cc_start: 0.8686 (mmm) cc_final: 0.8110 (mmm) REVERT: B 1141 PHE cc_start: 0.8283 (m-80) cc_final: 0.7642 (m-80) REVERT: B 1170 LYS cc_start: 0.6133 (mmmt) cc_final: 0.5654 (tmtt) REVERT: B 1179 PHE cc_start: 0.8523 (t80) cc_final: 0.8321 (t80) REVERT: B 1187 ILE cc_start: 0.8756 (mt) cc_final: 0.8234 (mt) REVERT: B 1191 MET cc_start: 0.8726 (mtt) cc_final: 0.8292 (mmm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0540 time to fit residues: 7.4950 Evaluate side-chains 72 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 126 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 49 optimal weight: 8.9990 chunk 197 optimal weight: 0.0050 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 177 optimal weight: 0.0000 chunk 38 optimal weight: 0.0670 chunk 189 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN B1008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.064545 restraints weight = 27030.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066378 restraints weight = 17303.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067689 restraints weight = 12543.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068562 restraints weight = 9986.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069196 restraints weight = 8480.545| |-----------------------------------------------------------------------------| r_work (final): 0.3355 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062327 restraints weight = 25389.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064063 restraints weight = 16847.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.065336 restraints weight = 12406.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.066210 restraints weight = 9864.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066833 restraints weight = 8352.764| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19894 Z= 0.122 Angle : 0.650 16.456 26888 Z= 0.323 Chirality : 0.042 0.394 2998 Planarity : 0.003 0.037 3314 Dihedral : 5.707 91.709 2694 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 are not related in a simple way. whole: 0.84 (0.17), residues: 2460 helix: 1.77 (0.14), residues: 1340 sheet: -0.02 (0.44), residues: 130 loop : -1.10 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.014 0.001 TYR B 405 PHE 0.024 0.002 PHE A 541 TRP 0.025 0.002 TRP A1063 HIS 0.007 0.001 HIS D1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (19882) covalent geometry : angle 0.64647 / 0.32 (26864) SS BOND : bond 0.00338 / 0.23 ( 12) SS BOND : angle 2.43297 / 1.72 ( 24) hydrogen bonds : bond 0.03524 / 2.31 ( 1109) hydrogen bonds : angle 4.18718 / 2.96 ( 3243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.22 seconds wall clock time: 36 minutes 41.51 seconds (2201.51 seconds total)