Starting phenix.real_space_refine on Sat Jul 4 08:11:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnn_26015/07_2026/7tnn_26015.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnn_26015/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tnn_26015/07_2026/7tnn_26015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnn_26015/07_2026/7tnn_26015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnn_26015/07_2026/7tnn_26015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnn_26015/07_2026/7tnn_26015.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnn_26015/07_2026/7tnn_26015.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnn_26015/07_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-6108/lib/python3.11/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: 4.06, per 1000 atoms: 0.21 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: 1.59 Conformation dependent library (CDL) restraints added in 838.7 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: 0.52 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: 3.36 Time building geometry restraints manager: 2.07 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 - 19.24: 11215 19.24 - 38.48: 422 38.48 - 57.72: 52 57.72 - 76.96: 10 76.96 - 96.20: 6 Dihedral angle restraints: 11705 sinusoidal: 4570 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 11702 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.510 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 10.688 96.196 7117 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/Z covalent geometry : bond 0.00520 / 0.24 (19872) covalent geometry : angle 0.91877 / 0.51 (26851) SS BOND : bond 0.00652 / 0.34 ( 12) SS BOND : angle 2.32865 / 1.63 ( 24) hydrogen bonds : bond 0.24390 / 15.66 ( 1100) hydrogen bonds : angle 7.32361 / 5.17 ( 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 : 0.744 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: 0.1371 time to fit residues: 145.3241 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 : 0.700 ------------------------------------------------------------------------------- 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... 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 791 ASN C1204 HIS D 411 ASN D 412 HIS 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099530 restraints weight = 38270.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102095 restraints weight = 22977.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103703 restraints weight = 16883.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104523 restraints weight = 14061.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105266 restraints weight = 12730.565| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19884 Z= 0.223 Angle : 0.670 10.160 26875 Z= 0.363 Chirality : 0.044 0.206 2998 Planarity : 0.005 0.059 3313 Dihedral : 6.243 92.104 2694 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.55 % Allowed : 13.62 % Favored : 82.83 % 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: -0.12 (0.16), residues: 2460 helix: 1.01 (0.13), residues: 1373 sheet: -0.56 (0.38), residues: 161 loop : -1.66 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1203 TYR 0.033 0.002 TYR D1173 PHE 0.025 0.002 PHE D1126 TRP 0.029 0.002 TRP D 766 HIS 0.018 0.002 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (19872) covalent geometry : angle 0.66824 / 0.36 (26851) SS BOND : bond 0.00854 / 0.64 ( 12) SS BOND : angle 1.85992 / 1.23 ( 24) hydrogen bonds : bond 0.05476 / 3.53 ( 1100) hydrogen bonds : angle 4.57940 / 3.25 ( 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 498 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 424 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8970 (pp) REVERT: A 516 SER cc_start: 0.8660 (p) cc_final: 0.8295 (t) REVERT: A 710 GLU cc_start: 0.7520 (tt0) cc_final: 0.7259 (mt-10) REVERT: A 732 TYR cc_start: 0.8992 (m-10) cc_final: 0.8659 (m-10) REVERT: A 1063 TRP cc_start: 0.6354 (m-10) cc_final: 0.5963 (m100) REVERT: A 1108 ILE cc_start: 0.8837 (pt) cc_final: 0.8437 (mt) REVERT: B 438 PHE cc_start: 0.7319 (p90) cc_final: 0.6900 (p90) REVERT: B 709 ASN cc_start: 0.8983 (t0) cc_final: 0.8597 (t0) REVERT: B 1199 MET cc_start: 0.7467 (mmm) cc_final: 0.7069 (mmp) REVERT: C 620 LEU cc_start: 0.9317 (tp) cc_final: 0.8945 (tp) REVERT: C 647 TYR cc_start: 0.6735 (p90) cc_final: 0.5901 (p90) REVERT: C 669 LYS cc_start: 0.7744 (ttpt) cc_final: 0.7327 (ptmt) REVERT: C 670 MET cc_start: 0.7975 (mmm) cc_final: 0.7152 (mmm) REVERT: C 761 LYS cc_start: 0.8181 (ttpm) cc_final: 0.7847 (pttp) REVERT: C 1080 ASP cc_start: 0.6975 (t70) cc_final: 0.6255 (p0) REVERT: C 1116 MET cc_start: 0.7615 (tpp) cc_final: 0.7257 (tpp) REVERT: C 1136 SER cc_start: 0.8815 (t) cc_final: 0.8586 (t) REVERT: C 1205 LYS cc_start: 0.7031 (mmmt) cc_final: 0.6428 (tptp) REVERT: D 728 ASP cc_start: 0.8182 (p0) cc_final: 0.7747 (t0) REVERT: D 1023 MET cc_start: 0.7327 (tpp) cc_final: 0.6994 (tpt) REVERT: D 1096 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7614 (t80) REVERT: D 1143 SER cc_start: 0.9230 (m) cc_final: 0.9013 (p) REVERT: D 1147 SER cc_start: 0.8960 (m) cc_final: 0.8651 (p) outliers start: 74 outliers final: 49 residues processed: 471 average time/residue: 0.1224 time to fit residues: 92.2877 Evaluate side-chains 389 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 338 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 595 SER 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 1204 HIS 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 604 VAL 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 489 ILE Chi-restraints excluded: chain C residue 528 CYS Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 693 VAL 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 1038 VAL Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain D residue 609 THR 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 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 1014 VAL 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: 1.9990 chunk 71 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 49 optimal weight: 0.0050 chunk 179 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A1204 HIS B 791 ASN ** C1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN ** D1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100541 restraints weight = 38481.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103221 restraints weight = 22567.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104944 restraints weight = 16333.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105998 restraints weight = 13461.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106532 restraints weight = 12009.215| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19884 Z= 0.137 Angle : 0.594 8.793 26875 Z= 0.315 Chirality : 0.041 0.212 2998 Planarity : 0.004 0.037 3313 Dihedral : 5.933 87.873 2694 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.50 % Allowed : 15.68 % Favored : 80.82 % 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: 0.54 (0.16), residues: 2460 helix: 1.74 (0.14), residues: 1360 sheet: -0.53 (0.38), residues: 152 loop : -1.61 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1203 TYR 0.039 0.001 TYR D1173 PHE 0.014 0.001 PHE C 658 TRP 0.030 0.001 TRP A 460 HIS 0.018 0.002 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (19872) covalent geometry : angle 0.59074 / 0.31 (26851) SS BOND : bond 0.00965 / 0.50 ( 12) SS BOND : angle 2.24537 / 1.49 ( 24) hydrogen bonds : bond 0.04512 / 2.93 ( 1100) hydrogen bonds : angle 4.22356 / 3.01 ( 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 464 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 391 time to evaluate : 0.825 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 498 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8885 (pp) REVERT: A 516 SER cc_start: 0.8636 (p) cc_final: 0.8246 (t) REVERT: A 619 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8346 (t0) REVERT: A 1063 TRP cc_start: 0.6299 (m-10) cc_final: 0.6006 (m100) REVERT: B 438 PHE cc_start: 0.7241 (p90) cc_final: 0.6796 (p90) REVERT: B 709 ASN cc_start: 0.9038 (t0) cc_final: 0.8775 (t0) REVERT: B 1020 PHE cc_start: 0.8043 (t80) cc_final: 0.7786 (t80) REVERT: B 1059 HIS cc_start: 0.6536 (p-80) cc_final: 0.6276 (p90) REVERT: B 1199 MET cc_start: 0.7531 (mmm) cc_final: 0.7059 (mmp) REVERT: C 619 ASN cc_start: 0.8403 (m-40) cc_final: 0.7455 (m-40) REVERT: C 620 LEU cc_start: 0.9337 (tp) cc_final: 0.9062 (tp) REVERT: C 647 TYR cc_start: 0.6680 (p90) cc_final: 0.5910 (p90) REVERT: C 670 MET cc_start: 0.8059 (mmm) cc_final: 0.7211 (mmm) REVERT: C 1116 MET cc_start: 0.7560 (tpp) cc_final: 0.7250 (tpp) REVERT: C 1136 SER cc_start: 0.8808 (t) cc_final: 0.8555 (t) REVERT: C 1205 LYS cc_start: 0.7022 (mmmt) cc_final: 0.6470 (tptp) REVERT: D 728 ASP cc_start: 0.8176 (p0) cc_final: 0.7767 (t0) REVERT: D 1096 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7605 (t80) REVERT: D 1147 SER cc_start: 0.8988 (m) cc_final: 0.8654 (p) outliers start: 73 outliers final: 47 residues processed: 432 average time/residue: 0.1149 time to fit residues: 80.8593 Evaluate side-chains 384 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 619 ASN Chi-restraints excluded: chain A residue 666 VAL 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 454 ASP 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 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 655 THR 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 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 647 TYR Chi-restraints excluded: chain D residue 649 THR 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 1184 LEU 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: 0.9990 chunk 118 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN B 587 GLN B 791 ASN C 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100239 restraints weight = 38543.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102887 restraints weight = 23015.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104587 restraints weight = 16826.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105619 restraints weight = 13988.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106065 restraints weight = 12522.520| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3745 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= 0.132 Angle : 0.588 10.720 26875 Z= 0.307 Chirality : 0.041 0.221 2998 Planarity : 0.004 0.042 3313 Dihedral : 5.782 87.773 2694 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.60 % Allowed : 16.45 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2460 helix: 1.96 (0.14), residues: 1367 sheet: -0.82 (0.38), residues: 161 loop : -1.55 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1203 TYR 0.041 0.001 TYR D1173 PHE 0.011 0.001 PHE C 658 TRP 0.017 0.001 TRP A 460 HIS 0.014 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19872) covalent geometry : angle 0.58547 / 0.31 (26851) SS BOND : bond 0.00291 / 0.17 ( 12) SS BOND : angle 1.81435 / 1.15 ( 24) hydrogen bonds : bond 0.04119 / 2.67 ( 1100) hydrogen bonds : angle 4.10953 / 2.93 ( 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 425 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 350 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 GLN cc_start: 0.7572 (pp30) cc_final: 0.7358 (pp30) REVERT: A 516 SER cc_start: 0.8640 (p) cc_final: 0.8214 (t) REVERT: A 1063 TRP cc_start: 0.6300 (m-10) cc_final: 0.5966 (m100) REVERT: B 438 PHE cc_start: 0.7185 (p90) cc_final: 0.6898 (p90) REVERT: B 709 ASN cc_start: 0.9045 (t0) cc_final: 0.8830 (t0) REVERT: B 746 VAL cc_start: 0.9166 (t) cc_final: 0.8827 (p) REVERT: B 1020 PHE cc_start: 0.8086 (t80) cc_final: 0.7860 (t80) REVERT: B 1059 HIS cc_start: 0.6446 (p-80) cc_final: 0.6137 (p90) REVERT: B 1199 MET cc_start: 0.7596 (mmm) cc_final: 0.7071 (mmp) REVERT: C 647 TYR cc_start: 0.6662 (p90) cc_final: 0.5615 (p90) REVERT: C 670 MET cc_start: 0.8006 (mmm) cc_final: 0.6604 (mmm) REVERT: C 1040 LYS cc_start: 0.3353 (OUTLIER) cc_final: 0.2730 (mttt) REVERT: C 1103 SER cc_start: 0.8060 (m) cc_final: 0.7794 (p) REVERT: C 1116 MET cc_start: 0.7557 (tpp) cc_final: 0.7250 (tpp) REVERT: C 1136 SER cc_start: 0.8814 (t) cc_final: 0.8541 (t) REVERT: C 1205 LYS cc_start: 0.7071 (mmmt) cc_final: 0.6519 (tptp) REVERT: D 728 ASP cc_start: 0.8184 (p0) cc_final: 0.7773 (t0) REVERT: D 1147 SER cc_start: 0.8948 (m) cc_final: 0.8665 (p) outliers start: 75 outliers final: 57 residues processed: 398 average time/residue: 0.1136 time to fit residues: 73.7359 Evaluate side-chains 392 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 334 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 569 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 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 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 693 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1030 ASP 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 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 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 1204 HIS Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR 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 718 CYS Chi-restraints excluded: chain D residue 720 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 1076 CYS Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU 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: 0.6980 chunk 127 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** C 619 ASN ** 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 = 0.3633 r_free = 0.3633 target = 0.126825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101487 restraints weight = 38514.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102785 restraints weight = 24105.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103337 restraints weight = 17455.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104065 restraints weight = 16241.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103976 restraints weight = 14666.851| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19884 Z= 0.143 Angle : 0.569 9.312 26875 Z= 0.298 Chirality : 0.041 0.223 2998 Planarity : 0.004 0.039 3313 Dihedral : 5.710 88.925 2694 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.32 % Allowed : 16.31 % Favored : 79.38 % 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: 0.89 (0.17), residues: 2460 helix: 2.09 (0.14), residues: 1366 sheet: -0.90 (0.38), residues: 159 loop : -1.49 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 453 TYR 0.035 0.001 TYR D1173 PHE 0.010 0.001 PHE D 574 TRP 0.012 0.001 TRP A 460 HIS 0.011 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (19872) covalent geometry : angle 0.56806 / 0.30 (26851) SS BOND : bond 0.00270 / 0.17 ( 12) SS BOND : angle 1.37571 / 0.91 ( 24) hydrogen bonds : bond 0.03977 / 2.57 ( 1100) hydrogen bonds : angle 4.03618 / 2.89 ( 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 447 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 357 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 SER cc_start: 0.8671 (p) cc_final: 0.8238 (t) REVERT: A 619 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8332 (t0) REVERT: A 1063 TRP cc_start: 0.6315 (m-10) cc_final: 0.6052 (m100) REVERT: A 1096 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: B 438 PHE cc_start: 0.7361 (p90) cc_final: 0.7039 (p90) REVERT: B 709 ASN cc_start: 0.9063 (t0) cc_final: 0.8850 (t0) REVERT: B 746 VAL cc_start: 0.9190 (t) cc_final: 0.8884 (p) REVERT: B 1185 SER cc_start: 0.9118 (t) cc_final: 0.8890 (p) REVERT: B 1199 MET cc_start: 0.7624 (mmm) cc_final: 0.7292 (mmp) REVERT: C 647 TYR cc_start: 0.6605 (p90) cc_final: 0.5969 (p90) REVERT: C 669 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7357 (mtpp) REVERT: C 670 MET cc_start: 0.7910 (mmm) cc_final: 0.7041 (mmm) REVERT: C 1009 MET cc_start: 0.8854 (mmm) cc_final: 0.8539 (mmm) REVERT: C 1040 LYS cc_start: 0.3674 (OUTLIER) cc_final: 0.3090 (mttt) REVERT: C 1103 SER cc_start: 0.8111 (m) cc_final: 0.7893 (p) REVERT: C 1116 MET cc_start: 0.7596 (tpp) cc_final: 0.7302 (tpp) REVERT: C 1136 SER cc_start: 0.8816 (t) cc_final: 0.8548 (t) REVERT: C 1205 LYS cc_start: 0.7012 (mmmt) cc_final: 0.6487 (tptp) REVERT: D 728 ASP cc_start: 0.8226 (p0) cc_final: 0.7777 (t0) REVERT: D 1147 SER cc_start: 0.8956 (m) cc_final: 0.8685 (p) outliers start: 90 outliers final: 65 residues processed: 413 average time/residue: 0.1147 time to fit residues: 76.5045 Evaluate side-chains 399 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 331 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 ILE 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 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 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 1030 ASP 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 425 CYS Chi-restraints excluded: chain C residue 435 HIS 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 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 708 MET 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 1076 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 609 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 148 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** C 619 ASN ** 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 = 0.3629 r_free = 0.3629 target = 0.126657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099723 restraints weight = 38468.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102301 restraints weight = 23085.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103981 restraints weight = 16842.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104807 restraints weight = 14006.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105575 restraints weight = 12660.839| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19884 Z= 0.136 Angle : 0.563 8.946 26875 Z= 0.294 Chirality : 0.041 0.229 2998 Planarity : 0.004 0.038 3313 Dihedral : 5.665 89.761 2694 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.88 % Allowed : 17.55 % Favored : 78.56 % 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: 0.90 (0.17), residues: 2460 helix: 2.12 (0.14), residues: 1368 sheet: -1.00 (0.37), residues: 166 loop : -1.51 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1005 TYR 0.030 0.001 TYR D1173 PHE 0.013 0.001 PHE A 623 TRP 0.012 0.001 TRP A 460 HIS 0.015 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (19872) covalent geometry : angle 0.56186 / 0.29 (26851) SS BOND : bond 0.00342 / 0.19 ( 12) SS BOND : angle 1.24410 / 0.83 ( 24) hydrogen bonds : bond 0.03861 / 2.50 ( 1100) hydrogen bonds : angle 4.00378 / 2.86 ( 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 437 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 356 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 SER cc_start: 0.8638 (p) cc_final: 0.8180 (t) REVERT: A 1063 TRP cc_start: 0.6304 (m-10) cc_final: 0.6039 (m100) REVERT: A 1096 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: B 438 PHE cc_start: 0.7345 (p90) cc_final: 0.7142 (p90) REVERT: B 709 ASN cc_start: 0.9033 (t0) cc_final: 0.8827 (t0) REVERT: B 746 VAL cc_start: 0.9194 (t) cc_final: 0.8914 (p) REVERT: B 1017 PHE cc_start: 0.7720 (t80) cc_final: 0.7447 (t80) REVERT: B 1104 SER cc_start: 0.8997 (m) cc_final: 0.8461 (t) REVERT: B 1185 SER cc_start: 0.9121 (t) cc_final: 0.8874 (p) REVERT: B 1199 MET cc_start: 0.7654 (mmm) cc_final: 0.7289 (mmp) REVERT: C 647 TYR cc_start: 0.6524 (p90) cc_final: 0.6092 (p90) REVERT: C 669 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7344 (mtpp) REVERT: C 670 MET cc_start: 0.7927 (mmm) cc_final: 0.7155 (mmm) REVERT: C 1040 LYS cc_start: 0.3733 (OUTLIER) cc_final: 0.3234 (mttt) REVERT: C 1116 MET cc_start: 0.7617 (tpp) cc_final: 0.7326 (tpp) REVERT: C 1136 SER cc_start: 0.8801 (t) cc_final: 0.8547 (t) REVERT: C 1205 LYS cc_start: 0.7103 (mmmt) cc_final: 0.6522 (tptp) REVERT: D 728 ASP cc_start: 0.8219 (p0) cc_final: 0.7746 (t0) REVERT: D 1147 SER cc_start: 0.8897 (m) cc_final: 0.8621 (p) outliers start: 81 outliers final: 63 residues processed: 411 average time/residue: 0.1216 time to fit residues: 81.7174 Evaluate side-chains 396 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 331 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 SER 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 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 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 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 1030 ASP 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 425 CYS Chi-restraints excluded: chain C residue 435 HIS 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 645 ILE Chi-restraints excluded: chain C residue 655 THR 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 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 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 654 SER 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 1009 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 170 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** C 619 ASN ** 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 = 0.3637 r_free = 0.3637 target = 0.127314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101671 restraints weight = 38658.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102886 restraints weight = 24403.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103215 restraints weight = 17764.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103950 restraints weight = 17161.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103980 restraints weight = 15247.558| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19884 Z= 0.125 Angle : 0.555 9.390 26875 Z= 0.289 Chirality : 0.040 0.228 2998 Planarity : 0.003 0.038 3313 Dihedral : 5.591 90.105 2694 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.65 % Allowed : 18.42 % Favored : 77.94 % 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: 2.17 (0.14), residues: 1367 sheet: -0.92 (0.38), residues: 164 loop : -1.48 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 715 TYR 0.027 0.001 TYR D1173 PHE 0.009 0.001 PHE C 658 TRP 0.014 0.001 TRP C 460 HIS 0.007 0.001 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (19872) covalent geometry : angle 0.55412 / 0.29 (26851) SS BOND : bond 0.00289 / 0.18 ( 12) SS BOND : angle 1.13370 / 0.75 ( 24) hydrogen bonds : bond 0.03731 / 2.42 ( 1100) hydrogen bonds : angle 3.93018 / 2.81 ( 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 431 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 355 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6750 (pmmt) REVERT: A 516 SER cc_start: 0.8617 (p) cc_final: 0.8121 (t) REVERT: A 629 MET cc_start: 0.5326 (ptt) cc_final: 0.5104 (ptm) REVERT: A 1063 TRP cc_start: 0.6336 (m-10) cc_final: 0.6073 (m100) REVERT: B 463 MET cc_start: 0.8190 (tpp) cc_final: 0.7863 (mtp) REVERT: B 709 ASN cc_start: 0.9058 (t0) cc_final: 0.8841 (t0) REVERT: B 746 VAL cc_start: 0.9216 (t) cc_final: 0.8950 (p) REVERT: B 1017 PHE cc_start: 0.7750 (t80) cc_final: 0.7509 (t80) REVERT: B 1104 SER cc_start: 0.8990 (m) cc_final: 0.8462 (t) REVERT: B 1185 SER cc_start: 0.9125 (t) cc_final: 0.8887 (p) REVERT: B 1199 MET cc_start: 0.7638 (mmm) cc_final: 0.7284 (mmp) REVERT: B 1204 HIS cc_start: 0.6117 (t-90) cc_final: 0.5656 (t-170) REVERT: C 647 TYR cc_start: 0.6468 (p90) cc_final: 0.6063 (p90) REVERT: C 669 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7333 (mtpp) REVERT: C 670 MET cc_start: 0.8042 (mmm) cc_final: 0.7309 (mmm) REVERT: C 1009 MET cc_start: 0.8843 (mmm) cc_final: 0.8514 (mmm) REVERT: C 1040 LYS cc_start: 0.3708 (OUTLIER) cc_final: 0.3147 (mttt) REVERT: C 1116 MET cc_start: 0.7625 (tpp) cc_final: 0.7361 (tpp) REVERT: C 1136 SER cc_start: 0.8844 (t) cc_final: 0.8575 (t) REVERT: C 1205 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6461 (tptp) REVERT: D 728 ASP cc_start: 0.8224 (p0) cc_final: 0.7764 (t0) REVERT: D 1147 SER cc_start: 0.8919 (m) cc_final: 0.8650 (p) outliers start: 76 outliers final: 62 residues processed: 405 average time/residue: 0.1234 time to fit residues: 80.8830 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 : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 ILE 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 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 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 454 ASP Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 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 784 THR Chi-restraints excluded: chain B residue 1030 ASP 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 645 ILE Chi-restraints excluded: chain C residue 655 THR 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 1038 VAL 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 1204 HIS 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 639 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 720 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 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 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: 0.5980 chunk 112 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN B 756 GLN C1204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101786 restraints weight = 38783.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102943 restraints weight = 24099.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103473 restraints weight = 17709.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104155 restraints weight = 16681.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104184 restraints weight = 14772.853| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19884 Z= 0.125 Angle : 0.565 10.522 26875 Z= 0.292 Chirality : 0.040 0.227 2998 Planarity : 0.004 0.042 3313 Dihedral : 5.546 90.227 2694 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.55 % Allowed : 18.66 % 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: 0.97 (0.17), residues: 2460 helix: 2.17 (0.14), residues: 1366 sheet: -0.94 (0.37), residues: 164 loop : -1.47 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 715 TYR 0.024 0.001 TYR D1173 PHE 0.014 0.001 PHE B1020 TRP 0.033 0.001 TRP A 460 HIS 0.023 0.002 HIS C1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (19872) covalent geometry : angle 0.56424 / 0.29 (26851) SS BOND : bond 0.00357 / 0.19 ( 12) SS BOND : angle 1.10176 / 0.71 ( 24) hydrogen bonds : bond 0.03701 / 2.40 ( 1100) hydrogen bonds : angle 3.95135 / 2.83 ( 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 429 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 355 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6754 (pmmt) REVERT: A 516 SER cc_start: 0.8610 (p) cc_final: 0.7816 (t) REVERT: A 519 ASP cc_start: 0.8039 (m-30) cc_final: 0.7620 (m-30) REVERT: A 629 MET cc_start: 0.5331 (ptt) cc_final: 0.5131 (ptm) REVERT: A 710 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7304 (mp0) REVERT: A 1063 TRP cc_start: 0.6354 (m-10) cc_final: 0.6136 (m100) REVERT: B 463 MET cc_start: 0.8135 (tpp) cc_final: 0.7859 (mtp) REVERT: B 587 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: B 709 ASN cc_start: 0.9066 (t0) cc_final: 0.8835 (t0) REVERT: B 714 GLN cc_start: 0.7048 (pp30) cc_final: 0.6846 (tm-30) REVERT: B 746 VAL cc_start: 0.9218 (t) cc_final: 0.8976 (p) REVERT: B 1017 PHE cc_start: 0.7749 (t80) cc_final: 0.7507 (t80) REVERT: B 1104 SER cc_start: 0.9003 (m) cc_final: 0.8482 (t) REVERT: B 1185 SER cc_start: 0.9154 (t) cc_final: 0.8899 (p) REVERT: B 1199 MET cc_start: 0.7623 (mmm) cc_final: 0.7267 (mmp) REVERT: B 1204 HIS cc_start: 0.6066 (t-90) cc_final: 0.5604 (t-170) REVERT: C 669 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7448 (mtpp) REVERT: C 670 MET cc_start: 0.7981 (mmm) cc_final: 0.7767 (mmm) REVERT: C 1009 MET cc_start: 0.8869 (mmm) cc_final: 0.8558 (mmm) REVERT: C 1040 LYS cc_start: 0.3438 (OUTLIER) cc_final: 0.3070 (mttt) REVERT: C 1116 MET cc_start: 0.7617 (tpp) cc_final: 0.7363 (tpp) REVERT: C 1136 SER cc_start: 0.8837 (t) cc_final: 0.8575 (t) REVERT: C 1205 LYS cc_start: 0.7183 (mmmt) cc_final: 0.6490 (tptp) REVERT: D 585 MET cc_start: 0.8815 (mmm) cc_final: 0.8489 (mmm) REVERT: D 728 ASP cc_start: 0.8250 (p0) cc_final: 0.7771 (t0) REVERT: D 1147 SER cc_start: 0.8898 (m) cc_final: 0.8658 (p) outliers start: 74 outliers final: 65 residues processed: 401 average time/residue: 0.1271 time to fit residues: 82.0785 Evaluate side-chains 405 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 337 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 ILE 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 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 GLN 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 784 THR Chi-restraints excluded: chain B residue 1030 ASP 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 645 ILE Chi-restraints excluded: chain C residue 655 THR 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 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 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 639 LEU 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 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 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1184 LEU 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: 6.9990 chunk 147 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3638 r_free = 0.3638 target = 0.127192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101932 restraints weight = 38540.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103042 restraints weight = 23842.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103281 restraints weight = 17670.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103830 restraints weight = 17332.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103994 restraints weight = 15433.929| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19884 Z= 0.126 Angle : 0.567 9.333 26875 Z= 0.293 Chirality : 0.040 0.225 2998 Planarity : 0.004 0.042 3313 Dihedral : 5.514 90.264 2694 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.60 % Allowed : 18.94 % Favored : 77.46 % 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: 0.98 (0.17), residues: 2460 helix: 2.18 (0.14), residues: 1359 sheet: -0.83 (0.37), residues: 168 loop : -1.46 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 594 TYR 0.024 0.001 TYR D1173 PHE 0.010 0.001 PHE B1179 TRP 0.034 0.001 TRP A 460 HIS 0.010 0.001 HIS C1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19872) covalent geometry : angle 0.56601 / 0.29 (26851) SS BOND : bond 0.00281 / 0.18 ( 12) SS BOND : angle 1.04452 / 0.68 ( 24) hydrogen bonds : bond 0.03701 / 2.40 ( 1100) hydrogen bonds : angle 3.95322 / 2.84 ( 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 428 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 353 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (pmmt) REVERT: A 516 SER cc_start: 0.8592 (p) cc_final: 0.8100 (t) REVERT: A 710 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7240 (mp0) REVERT: A 1009 MET cc_start: 0.6841 (tpp) cc_final: 0.6609 (tpp) REVERT: A 1063 TRP cc_start: 0.6397 (m-10) cc_final: 0.6154 (m100) REVERT: B 463 MET cc_start: 0.8136 (tpp) cc_final: 0.7849 (mtp) REVERT: B 587 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: B 709 ASN cc_start: 0.9075 (t0) cc_final: 0.8846 (t0) REVERT: B 714 GLN cc_start: 0.7016 (pp30) cc_final: 0.6623 (tm-30) REVERT: B 746 VAL cc_start: 0.9220 (t) cc_final: 0.8990 (p) REVERT: B 1017 PHE cc_start: 0.7780 (t80) cc_final: 0.7557 (t80) REVERT: B 1104 SER cc_start: 0.8996 (m) cc_final: 0.8462 (t) REVERT: B 1119 LEU cc_start: 0.7195 (mt) cc_final: 0.6839 (pp) REVERT: B 1185 SER cc_start: 0.9147 (t) cc_final: 0.8904 (p) REVERT: B 1199 MET cc_start: 0.7622 (mmm) cc_final: 0.7264 (mmp) REVERT: B 1204 HIS cc_start: 0.6044 (t-90) cc_final: 0.5588 (t-170) REVERT: C 645 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6736 (tt) REVERT: C 1009 MET cc_start: 0.8866 (mmm) cc_final: 0.8548 (mmm) REVERT: C 1040 LYS cc_start: 0.3610 (OUTLIER) cc_final: 0.3322 (mttt) REVERT: C 1116 MET cc_start: 0.7632 (tpp) cc_final: 0.7364 (tpp) REVERT: C 1136 SER cc_start: 0.8839 (t) cc_final: 0.8576 (t) REVERT: C 1205 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6631 (tmtt) REVERT: D 728 ASP cc_start: 0.8244 (p0) cc_final: 0.7767 (t0) REVERT: D 763 LYS cc_start: 0.9023 (tmtp) cc_final: 0.8798 (tmtt) REVERT: D 1023 MET cc_start: 0.7793 (mmm) cc_final: 0.7360 (tpt) REVERT: D 1147 SER cc_start: 0.8905 (m) cc_final: 0.8667 (p) outliers start: 75 outliers final: 60 residues processed: 400 average time/residue: 0.1282 time to fit residues: 82.5639 Evaluate side-chains 400 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 336 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 ILE 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 1105 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 GLN 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 784 THR Chi-restraints excluded: chain B residue 1030 ASP 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 645 ILE Chi-restraints excluded: chain C residue 655 THR 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 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 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 639 LEU 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 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 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL 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: 0.8980 chunk 109 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 242 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** 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 = 0.3613 r_free = 0.3613 target = 0.125390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100234 restraints weight = 38779.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101188 restraints weight = 24935.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101770 restraints weight = 18598.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102495 restraints weight = 16947.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102488 restraints weight = 15396.319| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19884 Z= 0.177 Angle : 0.605 9.164 26875 Z= 0.315 Chirality : 0.042 0.236 2998 Planarity : 0.004 0.038 3313 Dihedral : 5.647 92.048 2693 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.36 % Allowed : 18.94 % Favored : 77.70 % 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: 0.87 (0.17), residues: 2460 helix: 2.08 (0.14), residues: 1365 sheet: -0.84 (0.39), residues: 159 loop : -1.51 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 594 TYR 0.025 0.002 TYR C 647 PHE 0.014 0.001 PHE B1020 TRP 0.035 0.002 TRP A 460 HIS 0.008 0.001 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (19872) covalent geometry : angle 0.60468 / 0.31 (26851) SS BOND : bond 0.00398 / 0.25 ( 12) SS BOND : angle 1.10131 / 0.70 ( 24) hydrogen bonds : bond 0.03939 / 2.54 ( 1100) hydrogen bonds : angle 4.07489 / 2.94 ( 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 397 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 327 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7287 (tptt) REVERT: A 516 SER cc_start: 0.8601 (p) cc_final: 0.8125 (t) REVERT: A 1063 TRP cc_start: 0.6447 (m-10) cc_final: 0.6235 (m100) REVERT: A 1092 THR cc_start: 0.7324 (p) cc_final: 0.7020 (t) REVERT: B 463 MET cc_start: 0.8154 (tpp) cc_final: 0.7840 (mtp) REVERT: B 709 ASN cc_start: 0.9052 (t0) cc_final: 0.8814 (t0) REVERT: B 746 VAL cc_start: 0.9222 (t) cc_final: 0.9002 (p) REVERT: B 1017 PHE cc_start: 0.7761 (t80) cc_final: 0.7544 (t80) REVERT: B 1104 SER cc_start: 0.9100 (m) cc_final: 0.8596 (t) REVERT: B 1185 SER cc_start: 0.9152 (t) cc_final: 0.8898 (p) REVERT: B 1199 MET cc_start: 0.7630 (mmm) cc_final: 0.7313 (mmp) REVERT: C 585 MET cc_start: 0.9144 (mmt) cc_final: 0.8931 (mmt) REVERT: C 670 MET cc_start: 0.8012 (mmm) cc_final: 0.7691 (mmm) REVERT: C 1040 LYS cc_start: 0.3565 (OUTLIER) cc_final: 0.3265 (mttt) REVERT: C 1116 MET cc_start: 0.7619 (tpp) cc_final: 0.7376 (tpp) REVERT: C 1136 SER cc_start: 0.8831 (t) cc_final: 0.8577 (t) REVERT: C 1205 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6512 (tptp) REVERT: D 647 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: D 728 ASP cc_start: 0.8307 (p0) cc_final: 0.7755 (t0) REVERT: D 763 LYS cc_start: 0.9007 (tmtp) cc_final: 0.8738 (tmtt) REVERT: D 1147 SER cc_start: 0.8937 (m) cc_final: 0.8703 (p) outliers start: 70 outliers final: 60 residues processed: 374 average time/residue: 0.1239 time to fit residues: 76.1790 Evaluate side-chains 385 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 323 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 1105 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 527 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 784 THR Chi-restraints excluded: chain B residue 1030 ASP 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 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1038 VAL 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 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 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 639 LEU 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 713 GLU 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 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL 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 163 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 216 optimal weight: 0.0270 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1008 GLN B 714 GLN B1204 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN D 586 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098409 restraints weight = 38898.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099305 restraints weight = 25266.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099936 restraints weight = 19068.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100534 restraints weight = 17360.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100596 restraints weight = 15592.285| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19884 Z= 0.207 Angle : 0.639 12.919 26875 Z= 0.333 Chirality : 0.043 0.252 2998 Planarity : 0.004 0.040 3313 Dihedral : 5.851 92.905 2693 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.50 % Allowed : 18.99 % Favored : 77.51 % 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: 0.64 (0.17), residues: 2460 helix: 1.89 (0.14), residues: 1355 sheet: -0.81 (0.37), residues: 178 loop : -1.63 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 594 TYR 0.023 0.002 TYR C 647 PHE 0.014 0.002 PHE A 584 TRP 0.030 0.002 TRP A 460 HIS 0.008 0.001 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (19872) covalent geometry : angle 0.63818 / 0.33 (26851) SS BOND : bond 0.00449 / 0.28 ( 12) SS BOND : angle 1.19458 / 0.76 ( 24) hydrogen bonds : bond 0.04245 / 2.73 ( 1100) hydrogen bonds : angle 4.22202 / 3.04 ( 3219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3169.15 seconds wall clock time: 55 minutes 47.69 seconds (3347.69 seconds total)