Starting phenix.real_space_refine on Tue Jun 17 05:11:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnn_26015/06_2025/7tnn_26015.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnn_26015/06_2025/7tnn_26015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnn_26015/06_2025/7tnn_26015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnn_26015/06_2025/7tnn_26015.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnn_26015/06_2025/7tnn_26015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnn_26015/06_2025/7tnn_26015.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.13, per 1000 atoms: 0.57 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: 4.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 2.00 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: 6.02 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5955 1.34 - 1.47: 5182 1.47 - 1.60: 8507 1.60 - 1.72: 11 1.72 - 1.85: 217 Bond restraints: 19872 Sorted by residual: bond pdb=" CA ARG D 675 " pdb=" C ARG D 675 " ideal model delta sigma weight residual 1.522 1.565 -0.043 1.37e-02 5.33e+03 9.66e+00 bond pdb=" CG LEU A 704 " pdb=" CD1 LEU A 704 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.59e+00 bond pdb=" N3 CYZ D1301 " pdb=" S2 CYZ D1301 " ideal model delta sigma weight residual 1.644 1.601 0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" N3 CYZ A1302 " pdb=" S2 CYZ A1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" N3 CYZ B1302 " pdb=" S2 CYZ B1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 19867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 26424 3.05 - 6.11: 379 6.11 - 9.16: 44 9.16 - 12.21: 2 12.21 - 15.27: 2 Bond angle restraints: 26851 Sorted by residual: angle pdb=" C LEU B 596 " pdb=" N SER B 597 " pdb=" CA SER B 597 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ALA C 775 " pdb=" N LYS C 776 " pdb=" CA LYS C 776 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C THR D 784 " pdb=" N SER D 785 " pdb=" CA SER D 785 " ideal model delta sigma weight residual 121.31 128.47 -7.16 1.49e+00 4.50e-01 2.31e+01 angle pdb=" N SER D 785 " pdb=" CA SER D 785 " pdb=" C SER D 785 " ideal model delta sigma weight residual 110.35 116.87 -6.52 1.40e+00 5.10e-01 2.17e+01 angle pdb=" N ARG C 628 " pdb=" CA ARG C 628 " pdb=" CB ARG C 628 " ideal model delta sigma weight residual 110.49 102.74 7.75 1.69e+00 3.50e-01 2.10e+01 ... (remaining 26846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 11427 24.59 - 49.18: 337 49.18 - 73.78: 16 73.78 - 98.37: 13 98.37 - 122.96: 8 Dihedral angle restraints: 11801 sinusoidal: 4666 harmonic: 7135 Sorted by residual: dihedral pdb=" CA GLU C 627 " pdb=" C GLU C 627 " pdb=" N ARG C 628 " pdb=" CA ARG C 628 " ideal model delta harmonic sigma weight residual -180.00 -133.20 -46.80 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual -86.00 -168.23 82.23 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS D1039 " pdb=" SG CYS D1039 " pdb=" SG CYS D1067 " pdb=" CB CYS D1067 " ideal model delta sinusoidal sigma weight residual 93.00 26.80 66.20 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 11798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2439 0.066 - 0.132: 463 0.132 - 0.198: 77 0.198 - 0.264: 17 0.264 - 0.330: 2 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU D 639 " pdb=" CB LEU D 639 " pdb=" CD1 LEU D 639 " pdb=" CD2 LEU D 639 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE B 476 " pdb=" CA ILE B 476 " pdb=" CG1 ILE B 476 " pdb=" CG2 ILE B 476 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C8 CYZ C1301 " pdb=" C1 CYZ C1301 " pdb=" N1 CYZ C1301 " pdb=" N2 CYZ C1301 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2995 not shown) Planarity restraints: 3313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 627 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.19e+01 pdb=" C GLU C 627 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU C 627 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG C 628 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 783 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C LYS A 783 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 783 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 784 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 511 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C LYS A 511 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 511 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 512 " 0.013 2.00e-02 2.50e+03 ... (remaining 3310 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4431 2.79 - 3.31: 18560 3.31 - 3.84: 31745 3.84 - 4.37: 36648 4.37 - 4.90: 63222 Nonbonded interactions: 154606 Sorted by model distance: nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLU C 402 " pdb=" OH TYR C 450 " model vdw 2.273 3.040 nonbonded pdb=" O GLN D 642 " pdb=" OH TYR D 647 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 631 " pdb=" O ILE A 633 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU D 402 " pdb=" OH TYR D 450 " model vdw 2.285 3.040 ... (remaining 154601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1207 \ or resid 1302)) selection = (chain 'B' and (resid 394 through 549 or resid 564 through 626 or (resid 627 and \ (name N or name CA or name C or name O or name CB )) or resid 628 through 1207 \ or resid 1302)) selection = (chain 'C' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 819 or resid 1 \ 002 through 1207 or resid 1301)) selection = (chain 'D' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 819 or resid 1 \ 002 through 1207 or resid 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: 1.310 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.570 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 19884 Z= 0.241 Angle : 0.921 15.267 26875 Z= 0.507 Chirality : 0.056 0.330 2998 Planarity : 0.006 0.053 3313 Dihedral : 11.690 122.960 7213 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (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 TRP 0.033 0.003 TRP B1032 HIS 0.009 0.002 HIS C1081 PHE 0.028 0.003 PHE B 495 TYR 0.032 0.002 TYR A 702 ARG 0.007 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.24390 ( 1100) hydrogen bonds : angle 7.32361 ( 3219) SS BOND : bond 0.00652 ( 12) SS BOND : angle 2.32865 ( 24) covalent geometry : bond 0.00520 (19872) covalent geometry : angle 0.91877 (26851) *********************** 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 : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.8872 (m) cc_final: 0.8576 (m) REVERT: A 498 LEU cc_start: 0.9339 (pp) cc_final: 0.8793 (pp) REVERT: A 516 SER cc_start: 0.8787 (p) cc_final: 0.8454 (t) REVERT: A 592 SER cc_start: 0.8394 (m) cc_final: 0.7996 (p) REVERT: A 634 GLU cc_start: 0.8103 (pt0) cc_final: 0.7402 (tp30) REVERT: A 661 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7819 (mtt-85) REVERT: A 708 MET cc_start: 0.7054 (mtt) cc_final: 0.6319 (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: 0.8498 (mt) REVERT: A 1033 LEU cc_start: 0.8326 (tt) cc_final: 0.8029 (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: 0.6277 (m-10) REVERT: A 1171 ASN cc_start: 0.4647 (p0) cc_final: 0.4238 (t0) REVERT: B 438 PHE cc_start: 0.7437 (p90) cc_final: 0.7150 (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: 0.7591 (t80) REVERT: B 1029 THR cc_start: 0.8594 (t) cc_final: 0.8134 (p) REVERT: B 1185 SER cc_start: 0.9114 (t) cc_final: 0.8718 (p) REVERT: C 542 LEU cc_start: 0.9071 (tt) cc_final: 0.8832 (tp) REVERT: C 647 TYR cc_start: 0.6464 (p90) cc_final: 0.5409 (p90) REVERT: C 752 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8240 (mtpp) REVERT: C 1067 CYS cc_start: 0.5493 (p) cc_final: 0.5186 (t) REVERT: C 1116 MET cc_start: 0.7577 (tpp) cc_final: 0.7195 (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: 0.8210 (t80) REVERT: C 1205 LYS cc_start: 0.6716 (mmmt) cc_final: 0.6173 (tmtt) REVERT: D 486 GLU cc_start: 0.8271 (tp30) cc_final: 0.7797 (tp30) REVERT: D 635 SER cc_start: 0.7613 (t) cc_final: 0.7195 (p) REVERT: D 719 ASP cc_start: 0.6818 (p0) cc_final: 0.6498 (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: 0.7452 (m100) REVERT: D 1116 MET cc_start: 0.7333 (mtp) cc_final: 0.6676 (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: 0.8721 (p) outliers start: 7 outliers final: 1 residues processed: 694 average time/residue: 0.3151 time to fit residues: 329.8459 Evaluate side-chains 385 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 208 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A1053 ASN A1204 HIS B 747 ASN B 791 ASN B1071 ASN ** B1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 586 GLN C 642 GLN C 726 ASN 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** D1171 ASN D1198 HIS D1204 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102714 restraints weight = 37985.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105424 restraints weight = 22269.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107188 restraints weight = 16131.676| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19884 Z= 0.153 Angle : 0.634 9.213 26875 Z= 0.342 Chirality : 0.042 0.186 2998 Planarity : 0.005 0.062 3313 Dihedral : 9.025 109.220 2790 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.01 % Allowed : 13.91 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2460 helix: 1.26 (0.13), residues: 1374 sheet: -0.45 (0.38), residues: 162 loop : -1.62 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 766 HIS 0.019 0.002 HIS B1059 PHE 0.028 0.002 PHE D1126 TYR 0.032 0.002 TYR D1173 ARG 0.011 0.001 ARG C1203 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 1100) hydrogen bonds : angle 4.47409 ( 3219) SS BOND : bond 0.00385 ( 12) SS BOND : angle 1.61257 ( 24) covalent geometry : bond 0.00326 (19872) covalent geometry : angle 0.63259 (26851) *********************** 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 485 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 443 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8925 (pp) REVERT: A 516 SER cc_start: 0.8633 (p) cc_final: 0.8292 (t) REVERT: A 619 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8264 (t0) REVERT: A 710 GLU cc_start: 0.7461 (tt0) cc_final: 0.7194 (mt-10) REVERT: A 732 TYR cc_start: 0.8942 (m-10) cc_final: 0.8625 (m-10) REVERT: A 1171 ASN cc_start: 0.4769 (p0) cc_final: 0.4260 (t0) REVERT: B 438 PHE cc_start: 0.7337 (p90) cc_final: 0.6966 (p90) REVERT: C 620 LEU cc_start: 0.9263 (tp) cc_final: 0.8931 (tp) REVERT: C 647 TYR cc_start: 0.6584 (p90) cc_final: 0.4966 (p90) REVERT: C 670 MET cc_start: 0.7402 (mmt) cc_final: 0.6198 (mmm) REVERT: C 761 LYS cc_start: 0.8145 (ttpm) cc_final: 0.7828 (pttp) REVERT: C 1116 MET cc_start: 0.7552 (tpp) cc_final: 0.7179 (tpp) REVERT: C 1136 SER cc_start: 0.8816 (t) cc_final: 0.8566 (t) REVERT: C 1205 LYS cc_start: 0.6965 (mmmt) cc_final: 0.6448 (tptp) REVERT: D 651 ASP cc_start: 0.7729 (t0) cc_final: 0.7471 (t0) REVERT: D 728 ASP cc_start: 0.8193 (p0) cc_final: 0.7858 (t0) REVERT: D 1023 MET cc_start: 0.7228 (tpp) cc_final: 0.6894 (tpt) REVERT: D 1032 TRP cc_start: 0.7841 (m100) cc_final: 0.7605 (m100) REVERT: D 1096 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7617 (t80) REVERT: D 1147 SER cc_start: 0.8972 (m) cc_final: 0.8671 (p) outliers start: 42 outliers final: 20 residues processed: 467 average time/residue: 0.2794 time to fit residues: 205.8119 Evaluate side-chains 369 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 346 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 ASN 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 1207 LEU Chi-restraints excluded: chain B residue 425 CYS 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 1202 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 184 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN A1053 ASN B 791 ASN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1131 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1008 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098223 restraints weight = 38531.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100049 restraints weight = 24251.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100085 restraints weight = 17292.317| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19884 Z= 0.256 Angle : 0.683 9.722 26875 Z= 0.363 Chirality : 0.045 0.255 2998 Planarity : 0.005 0.044 3313 Dihedral : 8.871 108.103 2790 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.70 % Allowed : 15.30 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2460 helix: 1.49 (0.13), residues: 1362 sheet: -0.72 (0.38), residues: 158 loop : -1.59 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 460 HIS 0.016 0.002 HIS B1059 PHE 0.020 0.002 PHE A 682 TYR 0.037 0.002 TYR D1173 ARG 0.006 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 1100) hydrogen bonds : angle 4.47528 ( 3219) SS BOND : bond 0.00605 ( 12) SS BOND : angle 1.81548 ( 24) covalent geometry : bond 0.00592 (19872) covalent geometry : angle 0.68164 (26851) *********************** 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 454 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 2.001 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: 0.9007 (pp) REVERT: A 516 SER cc_start: 0.8689 (p) cc_final: 0.8304 (t) REVERT: A 732 TYR cc_start: 0.8990 (m-10) cc_final: 0.8715 (m-10) REVERT: A 1096 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: B 438 PHE cc_start: 0.7256 (p90) cc_final: 0.6847 (p90) REVERT: B 709 ASN cc_start: 0.9054 (t0) cc_final: 0.8778 (t0) REVERT: B 1020 PHE cc_start: 0.8114 (t80) cc_final: 0.7855 (t80) REVERT: B 1059 HIS cc_start: 0.6432 (p-80) cc_final: 0.6119 (p90) REVERT: B 1185 SER cc_start: 0.9140 (t) cc_final: 0.8866 (p) REVERT: C 620 LEU cc_start: 0.9363 (tp) cc_final: 0.9033 (tp) REVERT: C 647 TYR cc_start: 0.6485 (p90) cc_final: 0.5471 (p90) REVERT: C 761 LYS cc_start: 0.8199 (ttpm) cc_final: 0.7970 (pttp) REVERT: C 1059 HIS cc_start: 0.7975 (p90) cc_final: 0.7645 (p90) REVERT: C 1078 GLN cc_start: 0.6845 (pp30) cc_final: 0.6170 (mt0) REVERT: C 1116 MET cc_start: 0.7609 (tpp) cc_final: 0.7312 (tpp) REVERT: C 1136 SER cc_start: 0.8848 (t) cc_final: 0.8588 (t) REVERT: C 1205 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6470 (tptp) REVERT: D 635 SER cc_start: 0.8047 (t) cc_final: 0.7789 (p) REVERT: D 728 ASP cc_start: 0.8311 (p0) cc_final: 0.7779 (t0) REVERT: D 1147 SER cc_start: 0.9014 (m) cc_final: 0.8704 (p) outliers start: 98 outliers final: 70 residues processed: 418 average time/residue: 0.2653 time to fit residues: 178.2748 Evaluate side-chains 396 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 324 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 407 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL 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 800 VAL 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 425 CYS Chi-restraints excluded: chain B residue 445 VAL 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 620 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 784 THR 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 1127 TYR Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 542 LEU 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 693 VAL Chi-restraints excluded: chain C residue 736 THR 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 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 C residue 1195 LEU Chi-restraints excluded: chain D residue 529 ILE 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 674 MET 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 1055 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 231 optimal weight: 0.0970 chunk 163 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 227 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 209 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN C1204 HIS D 586 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101574 restraints weight = 38600.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103485 restraints weight = 24332.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103956 restraints weight = 16921.680| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19884 Z= 0.125 Angle : 0.597 10.666 26875 Z= 0.310 Chirality : 0.041 0.251 2998 Planarity : 0.004 0.036 3313 Dihedral : 8.199 100.288 2790 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.64 % Allowed : 17.27 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2460 helix: 1.95 (0.14), residues: 1370 sheet: -0.85 (0.35), residues: 176 loop : -1.52 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 460 HIS 0.014 0.002 HIS B1059 PHE 0.014 0.001 PHE C 658 TYR 0.040 0.001 TYR D1173 ARG 0.005 0.000 ARG C1064 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 1100) hydrogen bonds : angle 4.08945 ( 3219) SS BOND : bond 0.00295 ( 12) SS BOND : angle 1.98994 ( 24) covalent geometry : bond 0.00251 (19872) covalent geometry : angle 0.59381 (26851) *********************** 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 445 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 390 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9008 (pp) REVERT: A 508 GLN cc_start: 0.7347 (pp30) cc_final: 0.7137 (pp30) REVERT: A 516 SER cc_start: 0.8710 (p) cc_final: 0.8258 (t) REVERT: B 438 PHE cc_start: 0.7142 (p90) cc_final: 0.6855 (p90) REVERT: B 709 ASN cc_start: 0.9022 (t0) cc_final: 0.8814 (t0) REVERT: B 746 VAL cc_start: 0.9175 (t) cc_final: 0.8825 (p) REVERT: B 1020 PHE cc_start: 0.7951 (t80) cc_final: 0.7711 (t80) REVERT: B 1059 HIS cc_start: 0.6447 (p-80) cc_final: 0.5943 (p90) REVERT: C 647 TYR cc_start: 0.6385 (p90) cc_final: 0.5225 (p90) REVERT: C 670 MET cc_start: 0.7267 (mmt) cc_final: 0.6091 (mmm) REVERT: C 1078 GLN cc_start: 0.6903 (pp30) cc_final: 0.6027 (mt0) REVERT: C 1103 SER cc_start: 0.8126 (m) cc_final: 0.7876 (p) REVERT: C 1116 MET cc_start: 0.7588 (tpp) cc_final: 0.7265 (tpp) REVERT: C 1136 SER cc_start: 0.8827 (t) cc_final: 0.8543 (t) REVERT: C 1205 LYS cc_start: 0.7035 (mmmt) cc_final: 0.6469 (tptp) REVERT: D 635 SER cc_start: 0.7940 (t) cc_final: 0.7717 (p) REVERT: D 713 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7902 (tm-30) REVERT: D 728 ASP cc_start: 0.8237 (p0) cc_final: 0.7770 (t0) REVERT: D 1147 SER cc_start: 0.8979 (m) cc_final: 0.8704 (p) outliers start: 55 outliers final: 34 residues processed: 425 average time/residue: 0.2702 time to fit residues: 182.6065 Evaluate side-chains 376 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 341 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 597 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 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 1082 PHE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 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 1154 VAL Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 74 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 94 optimal weight: 0.0030 chunk 145 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 141 optimal weight: 0.2980 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100869 restraints weight = 38739.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102219 restraints weight = 24777.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102519 restraints weight = 18069.978| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19884 Z= 0.133 Angle : 0.582 10.970 26875 Z= 0.302 Chirality : 0.041 0.235 2998 Planarity : 0.003 0.041 3313 Dihedral : 8.050 98.360 2790 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.55 % Allowed : 17.41 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2460 helix: 2.06 (0.14), residues: 1368 sheet: -0.77 (0.39), residues: 156 loop : -1.52 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 460 HIS 0.012 0.002 HIS C1081 PHE 0.010 0.001 PHE C 658 TYR 0.033 0.001 TYR D1173 ARG 0.003 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 1100) hydrogen bonds : angle 4.02726 ( 3219) SS BOND : bond 0.00344 ( 12) SS BOND : angle 1.86168 ( 24) covalent geometry : bond 0.00300 (19872) covalent geometry : angle 0.57932 (26851) *********************** 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 428 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 354 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6714 (pmmt) REVERT: A 498 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8971 (pp) REVERT: A 516 SER cc_start: 0.8673 (p) cc_final: 0.8243 (t) REVERT: A 732 TYR cc_start: 0.8941 (m-10) cc_final: 0.8713 (m-10) REVERT: A 1096 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: B 438 PHE cc_start: 0.7235 (p90) cc_final: 0.6977 (p90) REVERT: B 670 MET cc_start: 0.8766 (mmm) cc_final: 0.7975 (mmt) REVERT: B 746 VAL cc_start: 0.9202 (t) cc_final: 0.8890 (p) REVERT: B 1010 LEU cc_start: 0.7919 (tt) cc_final: 0.7642 (tp) REVERT: B 1020 PHE cc_start: 0.8002 (t80) cc_final: 0.7752 (t80) REVERT: B 1104 SER cc_start: 0.8949 (m) cc_final: 0.8457 (t) REVERT: C 647 TYR cc_start: 0.6396 (p90) cc_final: 0.5565 (p90) REVERT: C 670 MET cc_start: 0.7235 (mmt) cc_final: 0.6745 (mmm) REVERT: C 705 GLU cc_start: 0.8509 (pm20) cc_final: 0.8219 (mm-30) REVERT: C 1009 MET cc_start: 0.8810 (mmm) cc_final: 0.8523 (mmm) REVERT: C 1040 LYS cc_start: 0.3302 (OUTLIER) cc_final: 0.2654 (mttt) REVERT: C 1078 GLN cc_start: 0.6878 (pp30) cc_final: 0.6121 (mt0) REVERT: C 1103 SER cc_start: 0.8222 (m) cc_final: 0.7985 (p) REVERT: C 1116 MET cc_start: 0.7607 (tpp) cc_final: 0.7290 (tpp) REVERT: C 1136 SER cc_start: 0.8821 (t) cc_final: 0.8544 (t) REVERT: C 1205 LYS cc_start: 0.6995 (mmmt) cc_final: 0.6468 (tptp) REVERT: D 635 SER cc_start: 0.7929 (t) cc_final: 0.7727 (p) REVERT: D 713 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7854 (tm-30) REVERT: D 728 ASP cc_start: 0.8258 (p0) cc_final: 0.7783 (t0) REVERT: D 1147 SER cc_start: 0.8964 (m) cc_final: 0.8705 (p) outliers start: 74 outliers final: 54 residues processed: 404 average time/residue: 0.2633 time to fit residues: 172.1966 Evaluate side-chains 393 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 666 VAL 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 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 519 ASP 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 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 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 647 TYR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 49 optimal weight: 0.0870 chunk 218 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 18 optimal weight: 0.0470 chunk 80 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN 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 = 0.3633 r_free = 0.3633 target = 0.126988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100877 restraints weight = 38598.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102520 restraints weight = 24764.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102822 restraints weight = 17681.006| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19884 Z= 0.132 Angle : 0.575 9.062 26875 Z= 0.298 Chirality : 0.041 0.247 2998 Planarity : 0.003 0.041 3313 Dihedral : 7.902 95.913 2790 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.50 % Allowed : 18.37 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2460 helix: 2.11 (0.14), residues: 1369 sheet: -0.80 (0.39), residues: 163 loop : -1.54 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 460 HIS 0.014 0.002 HIS B1059 PHE 0.009 0.001 PHE D1003 TYR 0.028 0.001 TYR D1173 ARG 0.003 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 1100) hydrogen bonds : angle 4.00332 ( 3219) SS BOND : bond 0.00255 ( 12) SS BOND : angle 1.44020 ( 24) covalent geometry : bond 0.00299 (19872) covalent geometry : angle 0.57361 (26851) *********************** 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 433 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6667 (pmmt) REVERT: A 498 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8971 (pp) REVERT: A 508 GLN cc_start: 0.7567 (pp30) cc_final: 0.7291 (pp30) REVERT: A 516 SER cc_start: 0.8664 (p) cc_final: 0.8189 (t) REVERT: A 629 MET cc_start: 0.5347 (ptt) cc_final: 0.5098 (ptm) REVERT: B 438 PHE cc_start: 0.7267 (p90) cc_final: 0.6972 (p90) REVERT: B 463 MET cc_start: 0.8061 (tpp) cc_final: 0.7791 (mtp) REVERT: B 746 VAL cc_start: 0.9195 (t) cc_final: 0.8911 (p) REVERT: B 1010 LEU cc_start: 0.7993 (tt) cc_final: 0.7697 (tp) REVERT: B 1017 PHE cc_start: 0.7741 (t80) cc_final: 0.7488 (t80) REVERT: B 1020 PHE cc_start: 0.8061 (t80) cc_final: 0.7808 (t80) REVERT: B 1059 HIS cc_start: 0.6295 (p-80) cc_final: 0.6090 (p90) REVERT: B 1104 SER cc_start: 0.8961 (m) cc_final: 0.8445 (t) REVERT: C 586 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8340 (mt0) REVERT: C 596 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8566 (mm) REVERT: C 647 TYR cc_start: 0.6338 (p90) cc_final: 0.5013 (p90) REVERT: C 670 MET cc_start: 0.7268 (mmt) cc_final: 0.6055 (mmm) REVERT: C 705 GLU cc_start: 0.8516 (pm20) cc_final: 0.8215 (mm-30) REVERT: C 1040 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.3004 (mttt) REVERT: C 1078 GLN cc_start: 0.6963 (pp30) cc_final: 0.6342 (mt0) REVERT: C 1103 SER cc_start: 0.8280 (m) cc_final: 0.8068 (p) REVERT: C 1116 MET cc_start: 0.7616 (tpp) cc_final: 0.7295 (tpp) REVERT: C 1136 SER cc_start: 0.8840 (t) cc_final: 0.8547 (t) REVERT: C 1205 LYS cc_start: 0.7058 (mmmt) cc_final: 0.6476 (tptp) REVERT: D 635 SER cc_start: 0.7924 (t) cc_final: 0.7720 (p) REVERT: D 713 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 728 ASP cc_start: 0.8281 (p0) cc_final: 0.7764 (t0) REVERT: D 763 LYS cc_start: 0.9029 (tmtp) cc_final: 0.8779 (tmtt) REVERT: D 1147 SER cc_start: 0.8971 (m) cc_final: 0.8698 (p) outliers start: 73 outliers final: 61 residues processed: 408 average time/residue: 0.2791 time to fit residues: 181.1026 Evaluate side-chains 402 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 336 time to evaluate : 2.072 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 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 586 GLN Chi-restraints excluded: chain C residue 596 LEU 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 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 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 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 162 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100173 restraints weight = 38224.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102621 restraints weight = 22961.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104268 restraints weight = 16974.002| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4308 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= 0.144 Angle : 0.583 9.183 26875 Z= 0.302 Chirality : 0.041 0.242 2998 Planarity : 0.004 0.041 3313 Dihedral : 7.867 94.778 2790 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.74 % Allowed : 18.37 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2460 helix: 2.12 (0.14), residues: 1361 sheet: -0.84 (0.39), residues: 163 loop : -1.52 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 460 HIS 0.012 0.002 HIS B1059 PHE 0.010 0.001 PHE A 584 TYR 0.032 0.001 TYR A 732 ARG 0.003 0.000 ARG D 661 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1100) hydrogen bonds : angle 4.01438 ( 3219) SS BOND : bond 0.00239 ( 12) SS BOND : angle 1.28225 ( 24) covalent geometry : bond 0.00334 (19872) covalent geometry : angle 0.58202 (26851) *********************** 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 423 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 345 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6654 (pmmt) REVERT: A 508 GLN cc_start: 0.7490 (pp30) cc_final: 0.7261 (pp30) REVERT: A 516 SER cc_start: 0.8632 (p) cc_final: 0.8153 (t) REVERT: A 629 MET cc_start: 0.5415 (ptt) cc_final: 0.5183 (ptm) REVERT: A 1096 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: B 438 PHE cc_start: 0.7229 (p90) cc_final: 0.6976 (p90) REVERT: B 463 MET cc_start: 0.8118 (tpp) cc_final: 0.7795 (mtp) REVERT: B 746 VAL cc_start: 0.9199 (t) cc_final: 0.8929 (p) REVERT: B 1010 LEU cc_start: 0.7942 (tt) cc_final: 0.7675 (tp) REVERT: B 1017 PHE cc_start: 0.7701 (t80) cc_final: 0.7469 (t80) REVERT: B 1020 PHE cc_start: 0.8068 (t80) cc_final: 0.7790 (t80) REVERT: B 1104 SER cc_start: 0.9025 (m) cc_final: 0.8506 (t) REVERT: B 1204 HIS cc_start: 0.6034 (t-90) cc_final: 0.5647 (t-170) REVERT: C 596 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8539 (mm) REVERT: C 647 TYR cc_start: 0.6323 (p90) cc_final: 0.5571 (p90) REVERT: C 669 LYS cc_start: 0.7736 (ttpt) cc_final: 0.7393 (mtpt) REVERT: C 670 MET cc_start: 0.7295 (mmt) cc_final: 0.6716 (mmt) REVERT: C 705 GLU cc_start: 0.8553 (pm20) cc_final: 0.8206 (mm-30) REVERT: C 1040 LYS cc_start: 0.3561 (OUTLIER) cc_final: 0.3018 (mttt) REVERT: C 1078 GLN cc_start: 0.7047 (pp30) cc_final: 0.6441 (mt0) REVERT: C 1103 SER cc_start: 0.8316 (m) cc_final: 0.8096 (p) REVERT: C 1116 MET cc_start: 0.7661 (tpp) cc_final: 0.7423 (tpp) REVERT: C 1136 SER cc_start: 0.8813 (t) cc_final: 0.8524 (t) REVERT: C 1205 LYS cc_start: 0.7081 (mmmt) cc_final: 0.6582 (tmtt) REVERT: D 713 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 728 ASP cc_start: 0.8285 (p0) cc_final: 0.7735 (t0) REVERT: D 763 LYS cc_start: 0.9022 (tmtp) cc_final: 0.8782 (tmtt) REVERT: D 783 LYS cc_start: 0.6391 (tppt) cc_final: 0.6187 (tppt) REVERT: D 1147 SER cc_start: 0.8972 (m) cc_final: 0.8707 (p) outliers start: 78 outliers final: 62 residues processed: 397 average time/residue: 0.2726 time to fit residues: 172.0108 Evaluate side-chains 394 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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 408 MET 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 1096 PHE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 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 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 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 408 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1076 CYS Chi-restraints excluded: chain D residue 1124 SER 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 164 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1204 HIS D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098060 restraints weight = 38922.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099186 restraints weight = 25281.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099714 restraints weight = 18611.776| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4510 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= 0.226 Angle : 0.655 11.250 26875 Z= 0.342 Chirality : 0.044 0.275 2998 Planarity : 0.004 0.040 3313 Dihedral : 8.246 98.466 2790 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.12 % Allowed : 18.47 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2460 helix: 1.89 (0.14), residues: 1346 sheet: -1.04 (0.39), residues: 166 loop : -1.55 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 460 HIS 0.011 0.002 HIS C1081 PHE 0.017 0.002 PHE A 682 TYR 0.034 0.002 TYR A 732 ARG 0.013 0.001 ARG C1203 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 1100) hydrogen bonds : angle 4.27135 ( 3219) SS BOND : bond 0.00383 ( 12) SS BOND : angle 1.46799 ( 24) covalent geometry : bond 0.00530 (19872) covalent geometry : angle 0.65394 (26851) *********************** 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 418 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 332 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6547 (pmmt) REVERT: A 458 LYS cc_start: 0.7661 (mmtm) cc_final: 0.7162 (tptt) REVERT: A 516 SER cc_start: 0.8621 (p) cc_final: 0.8135 (t) REVERT: A 1096 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: B 438 PHE cc_start: 0.7288 (p90) cc_final: 0.7033 (p90) REVERT: B 463 MET cc_start: 0.8173 (tpp) cc_final: 0.7851 (mtp) REVERT: B 714 GLN cc_start: 0.7023 (pp30) cc_final: 0.6809 (tm-30) REVERT: B 746 VAL cc_start: 0.9199 (t) cc_final: 0.8939 (p) REVERT: B 1010 LEU cc_start: 0.7990 (tt) cc_final: 0.7762 (tp) REVERT: B 1017 PHE cc_start: 0.7756 (t80) cc_final: 0.7510 (t80) REVERT: B 1104 SER cc_start: 0.9154 (m) cc_final: 0.8674 (t) REVERT: B 1185 SER cc_start: 0.9160 (t) cc_final: 0.8888 (p) REVERT: C 647 TYR cc_start: 0.6533 (p90) cc_final: 0.5286 (p90) REVERT: C 657 GLU cc_start: 0.6603 (tp30) cc_final: 0.6354 (tp30) REVERT: C 669 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7422 (mtpt) REVERT: C 670 MET cc_start: 0.7433 (mmt) cc_final: 0.6369 (mmm) REVERT: C 705 GLU cc_start: 0.8514 (pm20) cc_final: 0.8195 (mm-30) REVERT: C 1078 GLN cc_start: 0.7099 (pp30) cc_final: 0.6527 (mt0) REVERT: C 1136 SER cc_start: 0.8818 (t) cc_final: 0.8549 (t) REVERT: C 1205 LYS cc_start: 0.7127 (mmmt) cc_final: 0.6467 (tptp) REVERT: D 647 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: D 713 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 763 LYS cc_start: 0.9002 (tmtp) cc_final: 0.8690 (tmtt) REVERT: D 1147 SER cc_start: 0.8940 (m) cc_final: 0.8706 (p) outliers start: 86 outliers final: 68 residues processed: 392 average time/residue: 0.2687 time to fit residues: 167.6527 Evaluate side-chains 383 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 312 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 408 MET 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 592 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 723 VAL 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 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 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 427 ASP 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 742 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 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 408 MET Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1076 CYS Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 194 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 chunk 145 optimal weight: 0.0070 chunk 191 optimal weight: 0.0050 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN C1204 HIS D 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100496 restraints weight = 38331.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103103 restraints weight = 23246.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104797 restraints weight = 17165.513| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19884 Z= 0.119 Angle : 0.602 13.105 26875 Z= 0.309 Chirality : 0.041 0.244 2998 Planarity : 0.004 0.045 3313 Dihedral : 7.674 92.518 2790 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.97 % Allowed : 19.81 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2460 helix: 2.10 (0.14), residues: 1358 sheet: -0.82 (0.40), residues: 162 loop : -1.57 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 460 HIS 0.009 0.001 HIS C1081 PHE 0.013 0.001 PHE C 658 TYR 0.030 0.001 TYR D1173 ARG 0.010 0.000 ARG C1203 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1100) hydrogen bonds : angle 4.03596 ( 3219) SS BOND : bond 0.00233 ( 12) SS BOND : angle 1.17903 ( 24) covalent geometry : bond 0.00260 (19872) covalent geometry : angle 0.60158 (26851) *********************** 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 414 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 352 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.7590 (mmtm) cc_final: 0.7158 (tptt) REVERT: A 516 SER cc_start: 0.8632 (p) cc_final: 0.8153 (t) REVERT: B 463 MET cc_start: 0.8112 (tpp) cc_final: 0.7854 (mtp) REVERT: B 714 GLN cc_start: 0.7065 (pp30) cc_final: 0.6735 (tm-30) REVERT: B 746 VAL cc_start: 0.9194 (t) cc_final: 0.8944 (p) REVERT: B 1010 LEU cc_start: 0.8022 (tt) cc_final: 0.7797 (tp) REVERT: B 1017 PHE cc_start: 0.7710 (t80) cc_final: 0.7496 (t80) REVERT: B 1104 SER cc_start: 0.9105 (m) cc_final: 0.8575 (t) REVERT: B 1119 LEU cc_start: 0.7233 (mt) cc_final: 0.6884 (pp) REVERT: B 1185 SER cc_start: 0.9158 (t) cc_final: 0.8878 (p) REVERT: C 511 LYS cc_start: 0.7696 (mptp) cc_final: 0.7439 (tttm) REVERT: C 647 TYR cc_start: 0.6369 (p90) cc_final: 0.5355 (p90) REVERT: C 669 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7367 (mtpt) REVERT: C 670 MET cc_start: 0.7379 (mmt) cc_final: 0.6247 (mmm) REVERT: C 705 GLU cc_start: 0.8553 (pm20) cc_final: 0.8181 (mm-30) REVERT: C 1040 LYS cc_start: 0.3638 (OUTLIER) cc_final: 0.3310 (mttt) REVERT: C 1078 GLN cc_start: 0.7094 (pp30) cc_final: 0.6727 (mt0) REVERT: C 1080 ASP cc_start: 0.7060 (t70) cc_final: 0.6199 (m-30) REVERT: C 1205 LYS cc_start: 0.6997 (mmmt) cc_final: 0.6374 (tptp) REVERT: D 763 LYS cc_start: 0.8991 (tmtp) cc_final: 0.8684 (tmtt) REVERT: D 1147 SER cc_start: 0.8966 (m) cc_final: 0.8688 (p) outliers start: 62 outliers final: 50 residues processed: 393 average time/residue: 0.2803 time to fit residues: 175.9900 Evaluate side-chains 385 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 592 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 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 587 GLN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 546 PHE 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 408 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1076 CYS Chi-restraints excluded: chain D residue 1124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 169 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 208 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN 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 = 0.126989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099914 restraints weight = 38369.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102420 restraints weight = 23282.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104071 restraints weight = 17187.221| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19884 Z= 0.132 Angle : 0.613 13.439 26875 Z= 0.312 Chirality : 0.041 0.244 2998 Planarity : 0.004 0.049 3313 Dihedral : 7.562 91.726 2790 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.73 % Allowed : 20.72 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2460 helix: 2.12 (0.14), residues: 1357 sheet: -0.80 (0.40), residues: 162 loop : -1.55 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 460 HIS 0.010 0.001 HIS C1081 PHE 0.018 0.001 PHE C1082 TYR 0.028 0.001 TYR D1173 ARG 0.010 0.000 ARG C1203 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1100) hydrogen bonds : angle 4.02253 ( 3219) SS BOND : bond 0.00250 ( 12) SS BOND : angle 1.14261 ( 24) covalent geometry : bond 0.00303 (19872) covalent geometry : angle 0.61248 (26851) ********************** 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 398 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7259 (tptt) REVERT: A 516 SER cc_start: 0.8600 (p) cc_final: 0.8126 (t) REVERT: B 463 MET cc_start: 0.8110 (tpp) cc_final: 0.7819 (mtp) REVERT: B 714 GLN cc_start: 0.7046 (pp30) cc_final: 0.6702 (pp30) REVERT: B 746 VAL cc_start: 0.9208 (t) cc_final: 0.8983 (p) REVERT: B 1010 LEU cc_start: 0.8036 (tt) cc_final: 0.7799 (tp) REVERT: B 1104 SER cc_start: 0.9119 (m) cc_final: 0.8599 (t) REVERT: B 1119 LEU cc_start: 0.7265 (mt) cc_final: 0.6886 (pp) REVERT: B 1185 SER cc_start: 0.9168 (t) cc_final: 0.8874 (p) REVERT: C 511 LYS cc_start: 0.7618 (mptp) cc_final: 0.7395 (tttm) REVERT: C 647 TYR cc_start: 0.6361 (p90) cc_final: 0.5560 (p90) REVERT: C 670 MET cc_start: 0.7364 (mmt) cc_final: 0.7057 (mmm) REVERT: C 705 GLU cc_start: 0.8560 (pm20) cc_final: 0.8192 (mm-30) REVERT: C 1040 LYS cc_start: 0.3637 (OUTLIER) cc_final: 0.3356 (mttm) REVERT: C 1078 GLN cc_start: 0.7054 (pp30) cc_final: 0.6605 (mt0) REVERT: C 1205 LYS cc_start: 0.6992 (mmmt) cc_final: 0.6371 (tptp) REVERT: D 763 LYS cc_start: 0.8975 (tmtp) cc_final: 0.8696 (tmtt) REVERT: D 1147 SER cc_start: 0.8920 (m) cc_final: 0.8642 (p) outliers start: 57 outliers final: 50 residues processed: 377 average time/residue: 0.2684 time to fit residues: 162.7441 Evaluate side-chains 383 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 332 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 414 MET 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 748 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 634 GLU 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 408 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 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 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1076 CYS Chi-restraints excluded: chain D residue 1124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 92 optimal weight: 8.9990 chunk 246 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 231 optimal weight: 0.0570 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101655 restraints weight = 38530.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102686 restraints weight = 24613.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103146 restraints weight = 18052.191| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19884 Z= 0.131 Angle : 0.607 13.521 26875 Z= 0.308 Chirality : 0.041 0.240 2998 Planarity : 0.004 0.047 3313 Dihedral : 7.397 91.008 2790 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.73 % Allowed : 20.82 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2460 helix: 2.11 (0.14), residues: 1357 sheet: -0.72 (0.39), residues: 168 loop : -1.60 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 460 HIS 0.010 0.001 HIS C1081 PHE 0.018 0.001 PHE C1082 TYR 0.027 0.001 TYR D1173 ARG 0.010 0.000 ARG C1203 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1100) hydrogen bonds : angle 4.00997 ( 3219) SS BOND : bond 0.00251 ( 12) SS BOND : angle 1.09626 ( 24) covalent geometry : bond 0.00299 (19872) covalent geometry : angle 0.60605 (26851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6239.86 seconds wall clock time: 108 minutes 59.38 seconds (6539.38 seconds total)