Starting phenix.real_space_refine on Thu Mar 5 05:16:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnn_26015/03_2026/7tnn_26015.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnn_26015/03_2026/7tnn_26015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnn_26015/03_2026/7tnn_26015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnn_26015/03_2026/7tnn_26015.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnn_26015/03_2026/7tnn_26015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnn_26015/03_2026/7tnn_26015.cif" } resolution = 3.91 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 12564 2.51 5 N 3144 2.21 5 O 3591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19439 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4816 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 602} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4854 Classifications: {'peptide': 624} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 607} Chain breaks: 2 Chain: "D" Number of atoms: 4825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4825 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 603} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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: 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: 4.24, per 1000 atoms: 0.22 Number of scatterers: 19439 At special positions: 0 Unit cell: (126.16, 115.37, 137.78, 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 3591 8.00 N 3144 7.00 C 12564 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=2.04 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.02 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: 1.42 Conformation dependent library (CDL) restraints added in 838.5 milliseconds 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: 4552 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 25 sheets defined 56.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix 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 removed outlier: 3.945A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.508A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 removed outlier: 3.570A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.706A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 770 removed outlier: 3.715A pdb=" N LYS A 770 " --> pdb=" O TRP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 Processing helix chain 'A' and resid 1004 through 1029 Processing helix chain 'A' and resid 1051 through 1056 removed outlier: 3.543A pdb=" N GLU A1055 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A1056 " --> pdb=" O LYS A1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1051 through 1056' Processing helix chain 'A' and resid 1091 through 1104 Processing helix chain 'A' and resid 1104 through 1126 removed outlier: 3.998A pdb=" N PHE A1126 " --> pdb=" O ALA A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1160 Processing helix chain 'A' and resid 1176 through 1207 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.807A 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: 3.661A 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 565 through 569 removed outlier: 3.665A pdb=" N THR B 568 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN B 569 " --> pdb=" O GLU B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 565 through 569' Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 598 through 617 Processing helix chain 'B' and resid 619 through 626 Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.616A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.557A pdb=" N ARG B 715 " --> pdb=" O TYR B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.616A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 793 through 819 Processing helix chain 'B' and resid 1004 through 1029 Processing helix chain 'B' and resid 1051 through 1056 removed outlier: 3.962A pdb=" N GLU B1055 " --> pdb=" O LYS B1051 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B1056 " --> pdb=" O LYS B1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1051 through 1056' Processing helix chain 'B' and resid 1091 through 1104 Processing helix chain 'B' and resid 1104 through 1124 Processing helix chain 'B' and resid 1132 through 1159 Processing helix chain 'B' and resid 1176 through 1209 Processing helix chain 'C' and resid 410 through 413 removed outlier: 4.563A pdb=" N GLU C 413 " --> pdb=" O LYS C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 488 removed outlier: 4.198A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) 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: 3.660A pdb=" N THR C 568 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (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 removed outlier: 3.530A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.642A pdb=" N TYR C 673 " --> pdb=" O LYS C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.689A pdb=" N GLY C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.563A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 769 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.629A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1029 Processing helix chain 'C' and resid 1039 through 1043 removed outlier: 4.027A pdb=" N SER C1043 " --> pdb=" O LYS C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1054 removed outlier: 4.033A pdb=" N ASN C1053 " --> pdb=" O SER C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1104 Processing helix chain 'C' and resid 1104 through 1123 Processing helix chain 'C' and resid 1132 through 1159 Processing helix chain 'C' and resid 1176 through 1209 removed outlier: 3.528A pdb=" N GLN C1206 " --> pdb=" O ASP C1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.596A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.686A 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 565 through 569 removed outlier: 3.741A pdb=" N ASN D 569 " --> pdb=" O GLU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 618 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.509A pdb=" N PHE D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.517A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.574A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 769 Processing helix chain 'D' and resid 773 through 778 removed outlier: 4.233A pdb=" N ASP D 777 " --> pdb=" O CYS D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 821 Processing helix chain 'D' and resid 1004 through 1028 Processing helix chain 'D' and resid 1048 through 1053 removed outlier: 3.812A pdb=" N LYS D1051 " --> pdb=" O GLU D1048 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS D1052 " --> pdb=" O THR D1049 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D1053 " --> pdb=" O SER D1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1048 through 1053' Processing helix chain 'D' and resid 1092 through 1103 Processing helix chain 'D' and resid 1104 through 1123 Processing helix chain 'D' and resid 1131 through 1158 removed outlier: 3.957A pdb=" N LEU D1135 " --> pdb=" O HIS D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1207 removed outlier: 3.609A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 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: 4.791A pdb=" N ILE A 734 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR A 732 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N MET A 496 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS A 730 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.125A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1057 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 Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.605A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.605A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id=AB4, first strand: chain 'C' and resid 395 through 399 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 452 through 453 removed outlier: 3.598A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 489 through 498 removed outlier: 5.296A pdb=" N PHE C 491 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR C 736 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS C 493 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE C 734 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 648 removed outlier: 8.782A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1057 through 1060 Processing sheet with id=AC1, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.669A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.296A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1076 through 1078 removed outlier: 3.748A pdb=" N VAL D1056 " --> pdb=" O GLY D1037 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3219 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: 3.65 Time building geometry restraints manager: 1.96 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: 5955 1.34 - 1.47: 5182 1.47 - 1.60: 8507 1.60 - 1.72: 11 1.72 - 1.85: 217 Bond restraints: 19872 Sorted by residual: bond pdb=" CA ARG D 675 " pdb=" C ARG D 675 " ideal model delta sigma weight residual 1.522 1.565 -0.043 1.37e-02 5.33e+03 9.66e+00 bond pdb=" CG LEU A 704 " pdb=" CD1 LEU A 704 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.59e+00 bond pdb=" N3 CYZ D1301 " pdb=" S2 CYZ D1301 " ideal model delta sigma weight residual 1.644 1.601 0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" N3 CYZ A1302 " pdb=" S2 CYZ A1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" N3 CYZ B1302 " pdb=" S2 CYZ B1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 19867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 26424 3.05 - 6.11: 379 6.11 - 9.16: 44 9.16 - 12.21: 2 12.21 - 15.27: 2 Bond angle restraints: 26851 Sorted by residual: angle pdb=" C LEU B 596 " pdb=" N SER B 597 " pdb=" CA SER B 597 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ALA C 775 " pdb=" N LYS C 776 " pdb=" CA LYS C 776 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C THR D 784 " pdb=" N SER D 785 " pdb=" CA SER D 785 " ideal model delta sigma weight residual 121.31 128.47 -7.16 1.49e+00 4.50e-01 2.31e+01 angle pdb=" N SER D 785 " pdb=" CA SER D 785 " pdb=" C SER D 785 " ideal model delta sigma weight residual 110.35 116.87 -6.52 1.40e+00 5.10e-01 2.17e+01 angle pdb=" N ARG C 628 " pdb=" CA ARG C 628 " pdb=" CB ARG C 628 " ideal model delta sigma weight residual 110.49 102.74 7.75 1.69e+00 3.50e-01 2.10e+01 ... (remaining 26846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 11427 24.59 - 49.18: 337 49.18 - 73.78: 16 73.78 - 98.37: 13 98.37 - 122.96: 8 Dihedral angle restraints: 11801 sinusoidal: 4666 harmonic: 7135 Sorted by residual: dihedral pdb=" CA GLU C 627 " pdb=" C GLU C 627 " pdb=" N ARG C 628 " pdb=" CA ARG C 628 " ideal model delta harmonic sigma weight residual -180.00 -133.20 -46.80 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual -86.00 -168.23 82.23 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS D1039 " pdb=" SG CYS D1039 " pdb=" SG CYS D1067 " pdb=" CB CYS D1067 " ideal model delta sinusoidal sigma weight residual 93.00 26.80 66.20 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 11798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2439 0.066 - 0.132: 463 0.132 - 0.198: 77 0.198 - 0.264: 17 0.264 - 0.330: 2 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU D 639 " pdb=" CB LEU D 639 " pdb=" CD1 LEU D 639 " pdb=" CD2 LEU D 639 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE B 476 " pdb=" CA ILE B 476 " pdb=" CG1 ILE B 476 " pdb=" CG2 ILE B 476 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C8 CYZ C1301 " pdb=" C1 CYZ C1301 " pdb=" N1 CYZ C1301 " pdb=" N2 CYZ C1301 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2995 not shown) Planarity restraints: 3313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 627 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.19e+01 pdb=" C GLU C 627 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU C 627 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG C 628 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 783 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C LYS A 783 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 783 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 784 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 511 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C LYS A 511 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 511 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 512 " 0.013 2.00e-02 2.50e+03 ... (remaining 3310 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4431 2.79 - 3.31: 18560 3.31 - 3.84: 31745 3.84 - 4.37: 36648 4.37 - 4.90: 63222 Nonbonded interactions: 154606 Sorted by model distance: nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLU C 402 " pdb=" OH TYR C 450 " model vdw 2.273 3.040 nonbonded pdb=" O GLN D 642 " pdb=" OH TYR D 647 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 631 " pdb=" O ILE A 633 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU D 402 " pdb=" OH TYR D 450 " model vdw 2.285 3.040 ... (remaining 154601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1207 \ or resid 1302)) selection = (chain 'B' and (resid 394 through 549 or resid 564 through 626 or (resid 627 and \ (name N or name CA or name C or name O or name CB )) or resid 628 through 1207 \ or resid 1302)) selection = (chain 'C' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 819 or resid 1 \ 002 through 1207 or resid 1301)) selection = (chain 'D' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 819 or resid 1 \ 002 through 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.500 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.005 0.085 19884 Z= 0.241 Angle : 0.921 15.267 26875 Z= 0.507 Chirality : 0.056 0.330 2998 Planarity : 0.006 0.053 3313 Dihedral : 11.690 122.960 7213 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 0.34 % Allowed : 4.08 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.09 (0.13), residues: 2460 helix: -1.12 (0.10), residues: 1345 sheet: -0.28 (0.40), residues: 144 loop : -1.79 (0.17), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 599 TYR 0.032 0.002 TYR A 702 PHE 0.028 0.003 PHE B 495 TRP 0.033 0.003 TRP B1032 HIS 0.009 0.002 HIS C1081 Details of bonding type rmsd covalent geometry : bond 0.00520 (19872) covalent geometry : angle 0.91877 (26851) SS BOND : bond 0.00652 ( 12) SS BOND : angle 2.32865 ( 24) hydrogen bonds : bond 0.24390 ( 1100) hydrogen bonds : angle 7.32361 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 690 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.8873 (m) cc_final: 0.8581 (m) REVERT: A 498 LEU cc_start: 0.9339 (pp) cc_final: 0.8794 (pp) REVERT: A 516 SER cc_start: 0.8787 (p) cc_final: 0.8457 (t) REVERT: A 592 SER cc_start: 0.8394 (m) cc_final: 0.7997 (p) REVERT: A 661 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7820 (mtt-85) REVERT: A 708 MET cc_start: 0.7053 (mtt) cc_final: 0.6326 (mtt) REVERT: A 710 GLU cc_start: 0.7801 (tt0) cc_final: 0.7518 (mt-10) REVERT: A 1025 ILE cc_start: 0.8723 (mt) cc_final: 0.8497 (mt) REVERT: A 1033 LEU cc_start: 0.8326 (tt) cc_final: 0.8027 (pp) REVERT: A 1063 TRP cc_start: 0.6092 (m-10) cc_final: 0.5772 (m100) REVERT: A 1127 TYR cc_start: 0.6530 (m-10) cc_final: 0.6276 (m-10) REVERT: A 1171 ASN cc_start: 0.4647 (p0) cc_final: 0.4240 (t0) REVERT: B 438 PHE cc_start: 0.7437 (p90) cc_final: 0.7152 (p90) REVERT: B 527 MET cc_start: 0.7885 (ttp) cc_final: 0.7122 (mmm) REVERT: B 638 ASP cc_start: 0.7043 (t70) cc_final: 0.6771 (t70) REVERT: B 674 MET cc_start: 0.8193 (mmt) cc_final: 0.7925 (mmp) REVERT: B 1020 PHE cc_start: 0.7936 (t80) cc_final: 0.7590 (t80) REVERT: B 1029 THR cc_start: 0.8594 (t) cc_final: 0.8135 (p) REVERT: B 1185 SER cc_start: 0.9114 (t) cc_final: 0.8717 (p) REVERT: C 542 LEU cc_start: 0.9071 (tt) cc_final: 0.8831 (tp) REVERT: C 647 TYR cc_start: 0.6464 (p90) cc_final: 0.5475 (p90) REVERT: C 752 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8241 (mtpp) REVERT: C 1067 CYS cc_start: 0.5494 (p) cc_final: 0.5189 (t) REVERT: C 1116 MET cc_start: 0.7577 (tpp) cc_final: 0.7196 (tpp) REVERT: C 1136 SER cc_start: 0.8927 (t) cc_final: 0.8637 (m) REVERT: C 1179 PHE cc_start: 0.8411 (t80) cc_final: 0.8208 (t80) REVERT: C 1205 LYS cc_start: 0.6716 (mmmt) cc_final: 0.6172 (tmtt) REVERT: D 486 GLU cc_start: 0.8271 (tp30) cc_final: 0.7769 (tp30) REVERT: D 635 SER cc_start: 0.7613 (t) cc_final: 0.7217 (p) REVERT: D 719 ASP cc_start: 0.6818 (p0) cc_final: 0.6497 (p0) REVERT: D 728 ASP cc_start: 0.8029 (p0) cc_final: 0.7733 (t0) REVERT: D 1032 TRP cc_start: 0.7697 (m100) cc_final: 0.7467 (m100) REVERT: D 1116 MET cc_start: 0.7333 (mtp) cc_final: 0.6678 (mtt) REVERT: D 1126 PHE cc_start: 0.7186 (t80) cc_final: 0.6697 (t80) REVERT: D 1147 SER cc_start: 0.9140 (m) cc_final: 0.8720 (p) outliers start: 7 outliers final: 1 residues processed: 694 average time/residue: 0.1428 time to fit residues: 151.0094 Evaluate side-chains 386 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN A 619 ASN A1204 HIS B 747 ASN B 791 ASN B1008 GLN B1071 ASN B1131 HIS C 412 HIS C 586 GLN C 642 GLN C 726 ASN C 791 ASN C1053 ASN C1204 HIS D 411 ASN D 714 GLN D1008 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS D1204 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100054 restraints weight = 38234.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102527 restraints weight = 22954.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104159 restraints weight = 16806.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105129 restraints weight = 14017.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105622 restraints weight = 12595.792| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19884 Z= 0.221 Angle : 0.674 9.717 26875 Z= 0.365 Chirality : 0.044 0.198 2998 Planarity : 0.005 0.057 3313 Dihedral : 9.211 110.269 2790 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.26 % Allowed : 13.81 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.07 (0.16), residues: 2460 helix: 1.06 (0.13), residues: 1372 sheet: -0.48 (0.38), residues: 159 loop : -1.65 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1203 TYR 0.034 0.002 TYR D1173 PHE 0.030 0.002 PHE D1126 TRP 0.030 0.002 TRP D 766 HIS 0.018 0.002 HIS B1059 Details of bonding type rmsd covalent geometry : bond 0.00511 (19872) covalent geometry : angle 0.67244 (26851) SS BOND : bond 0.00520 ( 12) SS BOND : angle 1.79303 ( 24) hydrogen bonds : bond 0.05807 ( 1100) hydrogen bonds : angle 4.65639 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 426 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7168 (tp30) cc_final: 0.6950 (mm-30) REVERT: A 498 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8986 (pp) REVERT: A 516 SER cc_start: 0.8671 (p) cc_final: 0.8314 (t) REVERT: A 732 TYR cc_start: 0.9014 (m-10) cc_final: 0.8690 (m-10) REVERT: A 1063 TRP cc_start: 0.6315 (m-10) cc_final: 0.5957 (m100) REVERT: B 438 PHE cc_start: 0.7304 (p90) cc_final: 0.6845 (p90) REVERT: B 709 ASN cc_start: 0.8950 (t0) cc_final: 0.8578 (t0) REVERT: B 719 ASP cc_start: 0.7433 (p0) cc_final: 0.7152 (p0) REVERT: B 1199 MET cc_start: 0.7382 (mmm) cc_final: 0.7022 (mmp) REVERT: C 620 LEU cc_start: 0.9304 (tp) cc_final: 0.8921 (tp) REVERT: C 647 TYR cc_start: 0.6716 (p90) cc_final: 0.5894 (p90) REVERT: C 669 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7359 (ptmt) REVERT: C 670 MET cc_start: 0.7914 (mmm) cc_final: 0.7041 (mmm) REVERT: C 1078 GLN cc_start: 0.5688 (mt0) cc_final: 0.5445 (pp30) REVERT: C 1080 ASP cc_start: 0.7022 (t70) cc_final: 0.6387 (p0) REVERT: C 1116 MET cc_start: 0.7584 (tpp) cc_final: 0.7199 (tpp) REVERT: C 1136 SER cc_start: 0.8824 (t) cc_final: 0.8593 (t) REVERT: C 1205 LYS cc_start: 0.7063 (mmmt) cc_final: 0.6482 (tptp) REVERT: D 651 ASP cc_start: 0.7717 (t0) cc_final: 0.7502 (t0) REVERT: D 728 ASP cc_start: 0.8181 (p0) cc_final: 0.7776 (t0) REVERT: D 1096 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7622 (t80) REVERT: D 1147 SER cc_start: 0.8953 (m) cc_final: 0.8665 (p) outliers start: 68 outliers final: 45 residues processed: 467 average time/residue: 0.1280 time to fit residues: 95.5930 Evaluate side-chains 381 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1127 TYR Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 133 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 179 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 791 ASN D 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100987 restraints weight = 38401.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103603 restraints weight = 22505.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105326 restraints weight = 16336.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106352 restraints weight = 13477.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106990 restraints weight = 12036.501| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19884 Z= 0.139 Angle : 0.598 9.091 26875 Z= 0.317 Chirality : 0.041 0.207 2998 Planarity : 0.004 0.037 3313 Dihedral : 8.591 104.960 2790 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.60 % Allowed : 15.40 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.57 (0.16), residues: 2460 helix: 1.78 (0.14), residues: 1359 sheet: -0.70 (0.37), residues: 162 loop : -1.60 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1064 TYR 0.040 0.001 TYR D1173 PHE 0.014 0.001 PHE B 623 TRP 0.028 0.001 TRP A 460 HIS 0.018 0.002 HIS B1059 Details of bonding type rmsd covalent geometry : bond 0.00307 (19872) covalent geometry : angle 0.59459 (26851) SS BOND : bond 0.00461 ( 12) SS BOND : angle 2.17665 ( 24) hydrogen bonds : bond 0.04516 ( 1100) hydrogen bonds : angle 4.26091 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 390 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8929 (pp) REVERT: A 516 SER cc_start: 0.8645 (p) cc_final: 0.8257 (t) REVERT: A 619 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8350 (t0) REVERT: A 1063 TRP cc_start: 0.6284 (m-10) cc_final: 0.5978 (m100) REVERT: B 438 PHE cc_start: 0.7264 (p90) cc_final: 0.6894 (p90) REVERT: B 709 ASN cc_start: 0.9015 (t0) cc_final: 0.8737 (t0) REVERT: B 719 ASP cc_start: 0.7317 (p0) cc_final: 0.7048 (p0) REVERT: B 1020 PHE cc_start: 0.8039 (t80) cc_final: 0.7770 (t80) REVERT: B 1059 HIS cc_start: 0.6567 (p-80) cc_final: 0.6291 (p90) REVERT: B 1199 MET cc_start: 0.7523 (mmm) cc_final: 0.7018 (mmp) REVERT: C 619 ASN cc_start: 0.8400 (m-40) cc_final: 0.8142 (m-40) REVERT: C 620 LEU cc_start: 0.9334 (tp) cc_final: 0.9059 (tp) REVERT: C 647 TYR cc_start: 0.6685 (p90) cc_final: 0.5522 (p90) REVERT: C 670 MET cc_start: 0.8066 (mmm) cc_final: 0.7256 (mmm) REVERT: C 1116 MET cc_start: 0.7524 (tpp) cc_final: 0.7244 (tpp) REVERT: C 1136 SER cc_start: 0.8808 (t) cc_final: 0.8534 (t) REVERT: C 1205 LYS cc_start: 0.7044 (mmmt) cc_final: 0.6500 (tptp) REVERT: D 728 ASP cc_start: 0.8149 (p0) cc_final: 0.7770 (t0) REVERT: D 1023 MET cc_start: 0.7325 (tpt) cc_final: 0.7015 (tpp) REVERT: D 1096 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7604 (t80) REVERT: D 1147 SER cc_start: 0.8940 (m) cc_final: 0.8633 (p) outliers start: 75 outliers final: 49 residues processed: 433 average time/residue: 0.1153 time to fit residues: 82.4519 Evaluate side-chains 391 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1066 CYS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 204 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 230 optimal weight: 0.0020 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 791 ASN C 709 ASN D 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101795 restraints weight = 38268.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104520 restraints weight = 22590.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106221 restraints weight = 16363.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107065 restraints weight = 13551.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107769 restraints weight = 12213.533| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19884 Z= 0.121 Angle : 0.577 10.590 26875 Z= 0.301 Chirality : 0.041 0.214 2998 Planarity : 0.003 0.042 3313 Dihedral : 8.167 100.476 2790 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.31 % Allowed : 16.31 % Favored : 80.38 % 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: 0.82 (0.17), residues: 2460 helix: 2.05 (0.14), residues: 1364 sheet: -0.72 (0.36), residues: 173 loop : -1.58 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 453 TYR 0.040 0.001 TYR D1173 PHE 0.012 0.001 PHE C 658 TRP 0.016 0.001 TRP A 460 HIS 0.015 0.001 HIS B1059 Details of bonding type rmsd covalent geometry : bond 0.00261 (19872) covalent geometry : angle 0.57551 (26851) SS BOND : bond 0.00251 ( 12) SS BOND : angle 1.56965 ( 24) hydrogen bonds : bond 0.04015 ( 1100) hydrogen bonds : angle 4.05733 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8932 (pp) REVERT: A 508 GLN cc_start: 0.7504 (pp30) cc_final: 0.7301 (pp30) REVERT: A 516 SER cc_start: 0.8629 (p) cc_final: 0.8213 (t) REVERT: A 1063 TRP cc_start: 0.6275 (m-10) cc_final: 0.5961 (m100) REVERT: B 438 PHE cc_start: 0.7211 (p90) cc_final: 0.6933 (p90) REVERT: B 709 ASN cc_start: 0.9040 (t0) cc_final: 0.8838 (t0) REVERT: B 1020 PHE cc_start: 0.8030 (t80) cc_final: 0.7783 (t80) REVERT: B 1059 HIS cc_start: 0.6431 (p-80) cc_final: 0.6126 (p90) REVERT: B 1199 MET cc_start: 0.7586 (mmm) cc_final: 0.7065 (mmp) REVERT: C 619 ASN cc_start: 0.8406 (m-40) cc_final: 0.8090 (m-40) REVERT: C 620 LEU cc_start: 0.9317 (tp) cc_final: 0.9060 (tp) REVERT: C 647 TYR cc_start: 0.6471 (p90) cc_final: 0.5216 (p90) REVERT: C 669 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7342 (mtpp) REVERT: C 670 MET cc_start: 0.7787 (mmm) cc_final: 0.6220 (mmm) REVERT: C 705 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: C 1040 LYS cc_start: 0.3303 (OUTLIER) cc_final: 0.2699 (mttt) REVERT: C 1103 SER cc_start: 0.8029 (m) cc_final: 0.7765 (p) REVERT: C 1116 MET cc_start: 0.7502 (tpp) cc_final: 0.7246 (tpp) REVERT: C 1136 SER cc_start: 0.8815 (t) cc_final: 0.8543 (t) REVERT: C 1205 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6515 (tptp) REVERT: D 728 ASP cc_start: 0.8222 (p0) cc_final: 0.7812 (t0) REVERT: D 1147 SER cc_start: 0.8948 (m) cc_final: 0.8675 (p) outliers start: 69 outliers final: 50 residues processed: 408 average time/residue: 0.1207 time to fit residues: 79.9992 Evaluate side-chains 394 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 341 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1076 CYS Chi-restraints excluded: chain D residue 1154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 127 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 0.0060 chunk 244 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 overall best weight: 0.7076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 587 GLN C1204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101716 restraints weight = 38518.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104419 restraints weight = 22805.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106140 restraints weight = 16523.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106952 restraints weight = 13609.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107771 restraints weight = 12291.721| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19884 Z= 0.118 Angle : 0.555 10.926 26875 Z= 0.289 Chirality : 0.040 0.210 2998 Planarity : 0.003 0.041 3313 Dihedral : 7.952 97.621 2790 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.60 % Allowed : 16.74 % Favored : 79.66 % 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: 0.97 (0.17), residues: 2460 helix: 2.15 (0.14), residues: 1368 sheet: -0.88 (0.38), residues: 157 loop : -1.46 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.034 0.001 TYR D1173 PHE 0.021 0.001 PHE A 658 TRP 0.013 0.001 TRP A 460 HIS 0.011 0.001 HIS B1059 Details of bonding type rmsd covalent geometry : bond 0.00256 (19872) covalent geometry : angle 0.55406 (26851) SS BOND : bond 0.00211 ( 12) SS BOND : angle 1.36646 ( 24) hydrogen bonds : bond 0.03800 ( 1100) hydrogen bonds : angle 3.97565 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 368 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 SER cc_start: 0.8626 (p) cc_final: 0.8202 (t) REVERT: A 1063 TRP cc_start: 0.6248 (m-10) cc_final: 0.5967 (m100) REVERT: B 438 PHE cc_start: 0.7346 (p90) cc_final: 0.7022 (p90) REVERT: B 670 MET cc_start: 0.8755 (mmm) cc_final: 0.8029 (mmt) REVERT: B 746 VAL cc_start: 0.9166 (t) cc_final: 0.8838 (p) REVERT: B 1020 PHE cc_start: 0.8068 (t80) cc_final: 0.7789 (t80) REVERT: B 1199 MET cc_start: 0.7608 (mmm) cc_final: 0.7235 (mmp) REVERT: C 619 ASN cc_start: 0.8444 (m-40) cc_final: 0.8041 (m-40) REVERT: C 620 LEU cc_start: 0.9338 (tp) cc_final: 0.9052 (tp) REVERT: C 647 TYR cc_start: 0.6484 (p90) cc_final: 0.5354 (p90) REVERT: C 669 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7333 (mtpp) REVERT: C 670 MET cc_start: 0.7855 (mmm) cc_final: 0.6457 (mmm) REVERT: C 705 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: C 1009 MET cc_start: 0.8796 (mmm) cc_final: 0.8503 (mmm) REVERT: C 1040 LYS cc_start: 0.3681 (OUTLIER) cc_final: 0.3141 (mttt) REVERT: C 1103 SER cc_start: 0.8049 (m) cc_final: 0.7837 (p) REVERT: C 1116 MET cc_start: 0.7526 (tpp) cc_final: 0.7251 (tpp) REVERT: C 1136 SER cc_start: 0.8816 (t) cc_final: 0.8555 (t) REVERT: C 1205 LYS cc_start: 0.7056 (mmmt) cc_final: 0.6513 (tptp) REVERT: D 728 ASP cc_start: 0.8170 (p0) cc_final: 0.7804 (t0) REVERT: D 1147 SER cc_start: 0.8969 (m) cc_final: 0.8705 (p) outliers start: 75 outliers final: 56 residues processed: 416 average time/residue: 0.1247 time to fit residues: 83.9279 Evaluate side-chains 391 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 333 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1076 CYS Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 148 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C1204 HIS D 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097798 restraints weight = 39055.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098823 restraints weight = 24945.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099097 restraints weight = 18553.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099524 restraints weight = 17460.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099673 restraints weight = 16209.581| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19884 Z= 0.245 Angle : 0.654 8.421 26875 Z= 0.345 Chirality : 0.044 0.239 2998 Planarity : 0.004 0.040 3313 Dihedral : 8.353 101.596 2790 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.80 % Allowed : 16.93 % Favored : 78.27 % 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: 0.66 (0.17), residues: 2460 helix: 1.90 (0.14), residues: 1356 sheet: -1.12 (0.36), residues: 179 loop : -1.53 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 715 TYR 0.028 0.002 TYR D1173 PHE 0.022 0.002 PHE A 584 TRP 0.014 0.002 TRP C1063 HIS 0.017 0.002 HIS B1059 Details of bonding type rmsd covalent geometry : bond 0.00578 (19872) covalent geometry : angle 0.65337 (26851) SS BOND : bond 0.00513 ( 12) SS BOND : angle 1.39932 ( 24) hydrogen bonds : bond 0.04396 ( 1100) hydrogen bonds : angle 4.24676 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 338 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 SER cc_start: 0.8673 (p) cc_final: 0.8213 (t) REVERT: A 619 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8450 (t0) REVERT: A 1063 TRP cc_start: 0.6489 (m-10) cc_final: 0.6179 (m100) REVERT: A 1096 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: B 438 PHE cc_start: 0.7315 (p90) cc_final: 0.6850 (p90) REVERT: B 709 ASN cc_start: 0.9031 (t0) cc_final: 0.8828 (t0) REVERT: B 1017 PHE cc_start: 0.7737 (t80) cc_final: 0.7445 (t80) REVERT: B 1104 SER cc_start: 0.9093 (m) cc_final: 0.8622 (t) REVERT: B 1185 SER cc_start: 0.9148 (t) cc_final: 0.8893 (p) REVERT: B 1199 MET cc_start: 0.7595 (mmm) cc_final: 0.7285 (mmp) REVERT: C 620 LEU cc_start: 0.9373 (tp) cc_final: 0.8963 (tp) REVERT: C 647 TYR cc_start: 0.6631 (p90) cc_final: 0.5782 (p90) REVERT: C 657 GLU cc_start: 0.6581 (tp30) cc_final: 0.6376 (tp30) REVERT: C 670 MET cc_start: 0.8004 (mmm) cc_final: 0.7237 (mmm) REVERT: C 705 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: C 1103 SER cc_start: 0.8321 (m) cc_final: 0.8086 (p) REVERT: C 1116 MET cc_start: 0.7650 (tpp) cc_final: 0.7374 (tpp) REVERT: C 1136 SER cc_start: 0.8821 (t) cc_final: 0.8552 (t) REVERT: C 1205 LYS cc_start: 0.7109 (mmmt) cc_final: 0.6514 (tptp) REVERT: D 728 ASP cc_start: 0.8274 (p0) cc_final: 0.7739 (t0) REVERT: D 1147 SER cc_start: 0.8953 (m) cc_final: 0.8712 (p) outliers start: 100 outliers final: 75 residues processed: 405 average time/residue: 0.1210 time to fit residues: 79.8821 Evaluate side-chains 389 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 311 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1076 CYS Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 170 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 125 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN C1204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098893 restraints weight = 38866.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100139 restraints weight = 24785.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100383 restraints weight = 18344.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101086 restraints weight = 16827.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101168 restraints weight = 15825.959| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19884 Z= 0.173 Angle : 0.595 8.442 26875 Z= 0.312 Chirality : 0.042 0.263 2998 Planarity : 0.004 0.039 3313 Dihedral : 8.113 98.585 2790 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.08 % Allowed : 18.13 % Favored : 77.79 % 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: 0.72 (0.17), residues: 2460 helix: 1.98 (0.14), residues: 1349 sheet: -0.96 (0.38), residues: 171 loop : -1.56 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 715 TYR 0.027 0.002 TYR D1173 PHE 0.017 0.001 PHE B1200 TRP 0.029 0.001 TRP A 460 HIS 0.010 0.002 HIS C1081 Details of bonding type rmsd covalent geometry : bond 0.00402 (19872) covalent geometry : angle 0.59436 (26851) SS BOND : bond 0.00381 ( 12) SS BOND : angle 1.23206 ( 24) hydrogen bonds : bond 0.04110 ( 1100) hydrogen bonds : angle 4.14332 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 329 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6749 (pmmt) REVERT: A 508 GLN cc_start: 0.7582 (pp30) cc_final: 0.7303 (pp30) REVERT: A 516 SER cc_start: 0.8617 (p) cc_final: 0.8143 (t) REVERT: A 1063 TRP cc_start: 0.6452 (m-10) cc_final: 0.6197 (m100) REVERT: A 1171 ASN cc_start: 0.5071 (p0) cc_final: 0.4673 (m-40) REVERT: B 438 PHE cc_start: 0.7175 (p90) cc_final: 0.6875 (p90) REVERT: B 709 ASN cc_start: 0.9081 (t0) cc_final: 0.8839 (t0) REVERT: B 1017 PHE cc_start: 0.7759 (t80) cc_final: 0.7500 (t80) REVERT: B 1104 SER cc_start: 0.9082 (m) cc_final: 0.8582 (t) REVERT: B 1185 SER cc_start: 0.9145 (t) cc_final: 0.8923 (p) REVERT: B 1199 MET cc_start: 0.7591 (mmm) cc_final: 0.7285 (mmp) REVERT: C 586 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: C 620 LEU cc_start: 0.9378 (tp) cc_final: 0.9066 (tp) REVERT: C 647 TYR cc_start: 0.6515 (p90) cc_final: 0.5809 (p90) REVERT: C 670 MET cc_start: 0.7971 (mmm) cc_final: 0.7234 (mmm) REVERT: C 705 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: C 1040 LYS cc_start: 0.3676 (OUTLIER) cc_final: 0.3279 (mttt) REVERT: C 1116 MET cc_start: 0.7658 (tpp) cc_final: 0.7390 (tpp) REVERT: C 1136 SER cc_start: 0.8820 (t) cc_final: 0.8547 (t) REVERT: C 1205 LYS cc_start: 0.7106 (mmmt) cc_final: 0.6492 (tptp) REVERT: D 728 ASP cc_start: 0.8134 (p0) cc_final: 0.7686 (t0) REVERT: D 763 LYS cc_start: 0.9006 (tmtp) cc_final: 0.8654 (tmtt) REVERT: D 1147 SER cc_start: 0.8934 (m) cc_final: 0.8704 (p) outliers start: 85 outliers final: 65 residues processed: 386 average time/residue: 0.1199 time to fit residues: 75.5691 Evaluate side-chains 387 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 318 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 237 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B1204 HIS C1204 HIS D 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101172 restraints weight = 38529.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102684 restraints weight = 24423.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102884 restraints weight = 17670.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103475 restraints weight = 16958.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103589 restraints weight = 15369.612| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19884 Z= 0.125 Angle : 0.581 8.625 26875 Z= 0.301 Chirality : 0.041 0.250 2998 Planarity : 0.004 0.040 3313 Dihedral : 7.769 93.873 2790 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.55 % Allowed : 19.38 % Favored : 77.07 % 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: 2.05 (0.14), residues: 1368 sheet: -0.82 (0.39), residues: 164 loop : -1.56 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 594 TYR 0.025 0.001 TYR D1173 PHE 0.015 0.001 PHE A 658 TRP 0.031 0.001 TRP A 460 HIS 0.018 0.002 HIS C1204 Details of bonding type rmsd covalent geometry : bond 0.00277 (19872) covalent geometry : angle 0.57910 (26851) SS BOND : bond 0.00240 ( 12) SS BOND : angle 1.47168 ( 24) hydrogen bonds : bond 0.03824 ( 1100) hydrogen bonds : angle 4.01099 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 349 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6747 (pmmt) REVERT: A 458 LYS cc_start: 0.7700 (mmtm) cc_final: 0.7239 (tptt) REVERT: A 508 GLN cc_start: 0.7465 (pp30) cc_final: 0.7186 (pp30) REVERT: A 516 SER cc_start: 0.8581 (p) cc_final: 0.8099 (t) REVERT: A 619 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8364 (t0) REVERT: A 714 GLN cc_start: 0.7762 (mm110) cc_final: 0.7507 (mm110) REVERT: A 1063 TRP cc_start: 0.6406 (m-10) cc_final: 0.6149 (m100) REVERT: A 1171 ASN cc_start: 0.5030 (p0) cc_final: 0.4706 (m-40) REVERT: B 1017 PHE cc_start: 0.7725 (t80) cc_final: 0.7460 (t80) REVERT: B 1104 SER cc_start: 0.9074 (m) cc_final: 0.8567 (t) REVERT: B 1119 LEU cc_start: 0.7194 (mt) cc_final: 0.6799 (pp) REVERT: B 1185 SER cc_start: 0.9129 (t) cc_final: 0.8885 (p) REVERT: B 1199 MET cc_start: 0.7608 (mmm) cc_final: 0.7292 (mmp) REVERT: C 586 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: C 620 LEU cc_start: 0.9349 (tp) cc_final: 0.9071 (tp) REVERT: C 647 TYR cc_start: 0.6404 (p90) cc_final: 0.5829 (p90) REVERT: C 669 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7403 (mtpp) REVERT: C 670 MET cc_start: 0.7947 (mmm) cc_final: 0.7653 (mmm) REVERT: C 705 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: C 1009 MET cc_start: 0.8803 (mmm) cc_final: 0.8487 (mmm) REVERT: C 1040 LYS cc_start: 0.3696 (OUTLIER) cc_final: 0.3358 (mttt) REVERT: C 1116 MET cc_start: 0.7672 (tpp) cc_final: 0.7394 (tpp) REVERT: C 1136 SER cc_start: 0.8816 (t) cc_final: 0.8547 (t) REVERT: C 1205 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6608 (tmtt) REVERT: D 728 ASP cc_start: 0.8187 (p0) cc_final: 0.7689 (t0) REVERT: D 763 LYS cc_start: 0.8982 (tmtp) cc_final: 0.8686 (tmtt) REVERT: D 1147 SER cc_start: 0.8945 (m) cc_final: 0.8704 (p) outliers start: 74 outliers final: 59 residues processed: 394 average time/residue: 0.1230 time to fit residues: 78.4549 Evaluate side-chains 393 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 245 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 133 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN B1204 HIS C1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100059 restraints weight = 38481.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100890 restraints weight = 25602.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101223 restraints weight = 18218.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101597 restraints weight = 17939.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101754 restraints weight = 16434.146| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19884 Z= 0.170 Angle : 0.605 9.508 26875 Z= 0.315 Chirality : 0.042 0.262 2998 Planarity : 0.004 0.038 3313 Dihedral : 7.833 94.151 2790 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.60 % Allowed : 19.47 % Favored : 76.93 % 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: 0.73 (0.17), residues: 2460 helix: 1.97 (0.14), residues: 1355 sheet: -0.77 (0.39), residues: 163 loop : -1.59 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 594 TYR 0.020 0.002 TYR D1173 PHE 0.015 0.001 PHE B1020 TRP 0.032 0.002 TRP A 460 HIS 0.027 0.002 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00397 (19872) covalent geometry : angle 0.60395 (26851) SS BOND : bond 0.00256 ( 12) SS BOND : angle 1.39446 ( 24) hydrogen bonds : bond 0.03973 ( 1100) hydrogen bonds : angle 4.10944 ( 3219) *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 328 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6730 (pmmt) REVERT: A 458 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7263 (tptt) REVERT: A 508 GLN cc_start: 0.7488 (pp30) cc_final: 0.7218 (pp30) REVERT: A 516 SER cc_start: 0.8597 (p) cc_final: 0.8125 (t) REVERT: A 714 GLN cc_start: 0.7742 (mm110) cc_final: 0.7502 (mm110) REVERT: A 1009 MET cc_start: 0.6863 (tpp) cc_final: 0.6647 (tpp) REVERT: A 1171 ASN cc_start: 0.4981 (p0) cc_final: 0.4034 (t0) REVERT: B 1017 PHE cc_start: 0.7760 (t80) cc_final: 0.7510 (t80) REVERT: B 1104 SER cc_start: 0.9114 (m) cc_final: 0.8619 (t) REVERT: B 1185 SER cc_start: 0.9151 (t) cc_final: 0.8906 (p) REVERT: B 1199 MET cc_start: 0.7603 (mmm) cc_final: 0.7298 (mmp) REVERT: C 586 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: C 620 LEU cc_start: 0.9383 (tp) cc_final: 0.9041 (tp) REVERT: C 647 TYR cc_start: 0.6455 (p90) cc_final: 0.5851 (p90) REVERT: C 657 GLU cc_start: 0.6558 (tp30) cc_final: 0.6326 (tp30) REVERT: C 669 LYS cc_start: 0.7705 (ttpt) cc_final: 0.7429 (mtpp) REVERT: C 670 MET cc_start: 0.7952 (mmm) cc_final: 0.7622 (mmm) REVERT: C 702 TYR cc_start: 0.8180 (t80) cc_final: 0.7963 (t80) REVERT: C 705 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: C 1040 LYS cc_start: 0.3673 (OUTLIER) cc_final: 0.3298 (mttt) REVERT: C 1116 MET cc_start: 0.7616 (tpp) cc_final: 0.7368 (tpp) REVERT: C 1136 SER cc_start: 0.8807 (t) cc_final: 0.8543 (t) REVERT: C 1205 LYS cc_start: 0.7057 (mmmt) cc_final: 0.6403 (tptp) REVERT: D 728 ASP cc_start: 0.8182 (p0) cc_final: 0.7686 (t0) REVERT: D 763 LYS cc_start: 0.8953 (tmtp) cc_final: 0.8651 (tmtt) REVERT: D 1147 SER cc_start: 0.8929 (m) cc_final: 0.8698 (p) outliers start: 75 outliers final: 62 residues processed: 376 average time/residue: 0.1189 time to fit residues: 72.6775 Evaluate side-chains 382 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 316 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 152 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 222 optimal weight: 0.0270 chunk 136 optimal weight: 1.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B1204 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN C1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100810 restraints weight = 38479.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101700 restraints weight = 25084.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102008 restraints weight = 18488.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102486 restraints weight = 17571.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102716 restraints weight = 16130.550| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19884 Z= 0.136 Angle : 0.591 9.396 26875 Z= 0.305 Chirality : 0.041 0.250 2998 Planarity : 0.004 0.039 3313 Dihedral : 7.650 92.663 2790 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.26 % Allowed : 20.19 % Favored : 76.55 % 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: 0.81 (0.17), residues: 2460 helix: 2.05 (0.14), residues: 1356 sheet: -0.78 (0.39), residues: 164 loop : -1.57 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1203 TYR 0.030 0.001 TYR D1173 PHE 0.014 0.001 PHE A 658 TRP 0.033 0.001 TRP A 460 HIS 0.011 0.002 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00311 (19872) covalent geometry : angle 0.59043 (26851) SS BOND : bond 0.00217 ( 12) SS BOND : angle 1.18664 ( 24) hydrogen bonds : bond 0.03805 ( 1100) hydrogen bonds : angle 4.03936 ( 3219) ********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 325 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6740 (pmmt) REVERT: A 458 LYS cc_start: 0.7737 (mmtm) cc_final: 0.7215 (tptt) REVERT: A 508 GLN cc_start: 0.7490 (pp30) cc_final: 0.7230 (pp30) REVERT: A 516 SER cc_start: 0.8586 (p) cc_final: 0.8113 (t) REVERT: A 619 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8394 (t0) REVERT: A 714 GLN cc_start: 0.7783 (mm110) cc_final: 0.7540 (mm110) REVERT: A 1171 ASN cc_start: 0.5072 (p0) cc_final: 0.4640 (m-40) REVERT: B 714 GLN cc_start: 0.7077 (pp30) cc_final: 0.6819 (tm-30) REVERT: B 1017 PHE cc_start: 0.7754 (t80) cc_final: 0.7517 (t80) REVERT: B 1104 SER cc_start: 0.9094 (m) cc_final: 0.8570 (t) REVERT: B 1119 LEU cc_start: 0.7253 (mt) cc_final: 0.6860 (pp) REVERT: B 1185 SER cc_start: 0.9146 (t) cc_final: 0.8907 (p) REVERT: B 1199 MET cc_start: 0.7589 (mmm) cc_final: 0.7275 (mmp) REVERT: C 511 LYS cc_start: 0.7651 (mptp) cc_final: 0.7389 (tttm) REVERT: C 586 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: C 620 LEU cc_start: 0.9354 (tp) cc_final: 0.9039 (tp) REVERT: C 647 TYR cc_start: 0.6412 (p90) cc_final: 0.5835 (p90) REVERT: C 669 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7430 (mtpp) REVERT: C 670 MET cc_start: 0.7893 (mmm) cc_final: 0.7536 (mmm) REVERT: C 702 TYR cc_start: 0.8155 (t80) cc_final: 0.7932 (t80) REVERT: C 705 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: C 1040 LYS cc_start: 0.3624 (OUTLIER) cc_final: 0.3311 (mttt) REVERT: C 1116 MET cc_start: 0.7618 (tpp) cc_final: 0.7380 (tpp) REVERT: C 1136 SER cc_start: 0.8818 (t) cc_final: 0.8544 (t) REVERT: C 1205 LYS cc_start: 0.7054 (mmmt) cc_final: 0.6392 (tptp) REVERT: D 476 ILE cc_start: 0.8758 (mt) cc_final: 0.8552 (mm) REVERT: D 728 ASP cc_start: 0.8184 (p0) cc_final: 0.7683 (t0) REVERT: D 763 LYS cc_start: 0.8973 (tmtp) cc_final: 0.8667 (tmtt) REVERT: D 1147 SER cc_start: 0.8925 (m) cc_final: 0.8687 (p) outliers start: 68 outliers final: 58 residues processed: 366 average time/residue: 0.1172 time to fit residues: 69.5578 Evaluate side-chains 383 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 320 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 163 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 236 optimal weight: 0.4980 chunk 49 optimal weight: 0.0370 chunk 2 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 187 optimal weight: 0.0270 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102248 restraints weight = 38291.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103193 restraints weight = 24081.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103356 restraints weight = 17946.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103804 restraints weight = 17184.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103982 restraints weight = 16077.337| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19884 Z= 0.120 Angle : 0.593 13.187 26875 Z= 0.303 Chirality : 0.041 0.235 2998 Planarity : 0.004 0.039 3313 Dihedral : 7.432 90.625 2790 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.88 % Allowed : 20.86 % Favored : 76.26 % 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: 0.89 (0.17), residues: 2460 helix: 2.12 (0.14), residues: 1356 sheet: -0.66 (0.39), residues: 166 loop : -1.55 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.030 0.001 TYR D1173 PHE 0.015 0.001 PHE B1020 TRP 0.030 0.001 TRP A 460 HIS 0.016 0.002 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00262 (19872) covalent geometry : angle 0.59263 (26851) SS BOND : bond 0.00202 ( 12) SS BOND : angle 1.10895 ( 24) hydrogen bonds : bond 0.03698 ( 1100) hydrogen bonds : angle 3.98138 ( 3219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.98 seconds wall clock time: 54 minutes 46.18 seconds (3286.18 seconds total)