Starting phenix.real_space_refine on Thu Feb 5 15:46:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9e_71408/02_2026/9p9e_71408.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9e_71408/02_2026/9p9e_71408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9e_71408/02_2026/9p9e_71408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9e_71408/02_2026/9p9e_71408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9e_71408/02_2026/9p9e_71408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9e_71408/02_2026/9p9e_71408.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 132 5.16 5 Cl 4 4.86 5 C 11796 2.51 5 N 2916 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18100 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 1 Chain: "B" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 1 Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 1 Chain: "D" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Chain: "H" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "F" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "G" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CYZ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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: 3.93, per 1000 atoms: 0.22 Number of scatterers: 18100 At special positions: 0 Unit cell: (132.06, 114.39, 133.92, 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 132 16.00 O 3252 8.00 N 2916 7.00 C 11796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 795 " distance=2.04 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 795 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 764.4 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 25 sheets defined 58.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.596A pdb=" N LYS A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 568 Processing helix chain 'A' and resid 594 through 607 removed outlier: 4.200A pdb=" N SER A 598 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 645 Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.563A pdb=" N GLY A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 737 Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 839 removed outlier: 4.007A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 535 through 541 removed outlier: 4.546A pdb=" N PHE B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 568 removed outlier: 3.802A pdb=" N PHE B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 607 Processing helix chain 'B' and resid 617 through 640 Processing helix chain 'B' and resid 641 through 646 removed outlier: 3.753A pdb=" N PHE B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 675 through 684 removed outlier: 3.634A pdb=" N GLU B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 699 Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 727 through 736 removed outlier: 3.773A pdb=" N GLN B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 779 through 790 Processing helix chain 'B' and resid 810 through 813 Processing helix chain 'B' and resid 814 through 839 removed outlier: 4.175A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 445 through 459 Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 535 through 541 removed outlier: 4.598A pdb=" N PHE C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 566 removed outlier: 3.881A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 563 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 607 Processing helix chain 'C' and resid 617 through 647 removed outlier: 3.667A pdb=" N ILE C 633 " --> pdb=" O PHE C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 663 Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 686 through 699 Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 764 through 778 Processing helix chain 'C' and resid 779 through 790 Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 839 removed outlier: 3.917A pdb=" N PHE C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 839 " --> pdb=" O GLU C 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 437 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 445 through 459 removed outlier: 3.784A pdb=" N LYS D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 535 through 541 removed outlier: 4.544A pdb=" N PHE D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 568 Processing helix chain 'D' and resid 595 through 607 Processing helix chain 'D' and resid 617 through 640 Processing helix chain 'D' and resid 657 through 664 removed outlier: 4.119A pdb=" N GLN D 664 " --> pdb=" O ASP D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 683 Processing helix chain 'D' and resid 686 through 699 Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 727 through 735 Processing helix chain 'D' and resid 764 through 778 Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 790 through 793 removed outlier: 4.061A pdb=" N GLY D 793 " --> pdb=" O TYR D 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 790 through 793' Processing helix chain 'D' and resid 810 through 813 Processing helix chain 'D' and resid 814 through 839 removed outlier: 3.638A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 29 Processing helix chain 'H' and resid 95 through 105 Processing helix chain 'H' and resid 105 through 125 Processing helix chain 'H' and resid 132 through 160 Processing helix chain 'H' and resid 177 through 210 removed outlier: 3.536A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 29 removed outlier: 4.011A pdb=" N LEU F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 128 Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.829A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 208 removed outlier: 3.588A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 29 removed outlier: 3.695A pdb=" N LEU G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 160 Processing helix chain 'G' and resid 177 through 208 removed outlier: 3.639A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 29 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.540A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.578A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 466 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AA4, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.790A pdb=" N MET A 518 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 527 removed outlier: 4.308A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 705 removed outlier: 8.734A pdb=" N THR A 705 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR A 671 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 462 through 466 removed outlier: 3.592A pdb=" N ILE B 496 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA9, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=AB1, first strand: chain 'B' and resid 518 through 520 removed outlier: 3.899A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 524 through 527 removed outlier: 4.047A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 704 through 705 removed outlier: 8.022A pdb=" N THR B 705 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR B 671 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 462 through 466 removed outlier: 6.122A pdb=" N VAL C 417 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA C 465 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL C 419 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 511 through 513 Processing sheet with id=AB6, first strand: chain 'C' and resid 518 through 520 removed outlier: 3.751A pdb=" N MET C 518 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 704 through 705 removed outlier: 9.051A pdb=" N THR C 705 " --> pdb=" O TYR C 669 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR C 671 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N LEU C 672 " --> pdb=" O GLU C 727 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 462 through 466 removed outlier: 3.642A pdb=" N THR D 421 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AC1, first strand: chain 'D' and resid 511 through 520 removed outlier: 7.672A pdb=" N SER D 514 " --> pdb=" O THR D 758 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR D 758 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL D 756 " --> pdb=" O PRO D 516 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 524 through 527 removed outlier: 4.076A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 704 through 705 removed outlier: 8.851A pdb=" N THR D 705 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR D 671 " --> pdb=" O THR D 705 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AC5, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.750A pdb=" N MET F 58 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC7, first strand: chain 'E' and resid 78 through 79 1064 hydrogen bonds defined for protein. 3054 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 16 1.19 - 1.36: 5523 1.36 - 1.52: 7870 1.52 - 1.68: 4887 1.68 - 1.85: 220 Bond restraints: 18516 Sorted by residual: bond pdb=" C4 CYZ A 902 " pdb=" C5 CYZ A 902 " ideal model delta sigma weight residual 1.512 1.030 0.482 2.00e-02 2.50e+03 5.81e+02 bond pdb=" C4 CYZ B 903 " pdb=" C5 CYZ B 903 " ideal model delta sigma weight residual 1.512 1.030 0.482 2.00e-02 2.50e+03 5.81e+02 bond pdb=" C4 CYZ D 902 " pdb=" C5 CYZ D 902 " ideal model delta sigma weight residual 1.512 1.032 0.480 2.00e-02 2.50e+03 5.76e+02 bond pdb=" C4 CYZ B 902 " pdb=" C5 CYZ B 902 " ideal model delta sigma weight residual 1.512 1.033 0.479 2.00e-02 2.50e+03 5.74e+02 bond pdb=" C5 CYZ B 903 " pdb=" C6 CYZ B 903 " ideal model delta sigma weight residual 1.553 1.075 0.478 2.00e-02 2.50e+03 5.70e+02 ... (remaining 18511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 24901 4.44 - 8.88: 97 8.88 - 13.31: 6 13.31 - 17.75: 12 17.75 - 22.19: 4 Bond angle restraints: 25020 Sorted by residual: angle pdb=" C1 CYZ B 903 " pdb=" C2 CYZ B 903 " pdb=" C3 CYZ B 903 " ideal model delta sigma weight residual 106.92 129.11 -22.19 3.00e+00 1.11e-01 5.47e+01 angle pdb=" C1 CYZ A 902 " pdb=" C2 CYZ A 902 " pdb=" C3 CYZ A 902 " ideal model delta sigma weight residual 106.92 128.45 -21.53 3.00e+00 1.11e-01 5.15e+01 angle pdb=" C1 CYZ D 902 " pdb=" C2 CYZ D 902 " pdb=" C3 CYZ D 902 " ideal model delta sigma weight residual 106.92 128.20 -21.28 3.00e+00 1.11e-01 5.03e+01 angle pdb=" C1 CYZ B 902 " pdb=" C2 CYZ B 902 " pdb=" C3 CYZ B 902 " ideal model delta sigma weight residual 106.92 128.04 -21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" O3 CYZ A 902 " pdb=" S2 CYZ A 902 " pdb=" O4 CYZ A 902 " ideal model delta sigma weight residual 118.35 100.67 17.68 3.00e+00 1.11e-01 3.47e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 10470 23.80 - 47.61: 372 47.61 - 71.41: 36 71.41 - 95.21: 27 95.21 - 119.02: 8 Dihedral angle restraints: 10913 sinusoidal: 4317 harmonic: 6596 Sorted by residual: dihedral pdb=" CB CYS B 740 " pdb=" SG CYS B 740 " pdb=" SG CYS B 795 " pdb=" CB CYS B 795 " ideal model delta sinusoidal sigma weight residual 93.00 143.76 -50.76 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA PHE C 563 " pdb=" C PHE C 563 " pdb=" N LEU C 564 " pdb=" CA LEU C 564 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ARG A 737 " pdb=" C ARG A 737 " pdb=" N LYS A 738 " pdb=" CA LYS A 738 " ideal model delta harmonic sigma weight residual 180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.426: 2785 0.426 - 0.852: 7 0.852 - 1.279: 0 1.279 - 1.705: 0 1.705 - 2.131: 8 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C5 CYZ B 902 " pdb=" C4 CYZ B 902 " pdb=" C6 CYZ B 902 " pdb=" C7 CYZ B 902 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.13 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" C5 CYZ A 902 " pdb=" C4 CYZ A 902 " pdb=" C6 CYZ A 902 " pdb=" C7 CYZ A 902 " both_signs ideal model delta sigma weight residual False 3.31 1.18 2.13 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" C5 CYZ B 903 " pdb=" C4 CYZ B 903 " pdb=" C6 CYZ B 903 " pdb=" C7 CYZ B 903 " both_signs ideal model delta sigma weight residual False 3.31 1.18 2.13 2.00e-01 2.50e+01 1.13e+02 ... (remaining 2797 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 632 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LEU C 632 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU C 632 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE C 633 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 787 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LYS A 787 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS A 787 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP A 788 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 111 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C SER F 111 " 0.047 2.00e-02 2.50e+03 pdb=" O SER F 111 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL F 112 " -0.016 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 217 2.65 - 3.21: 18084 3.21 - 3.77: 28627 3.77 - 4.34: 38769 4.34 - 4.90: 63429 Nonbonded interactions: 149126 Sorted by model distance: nonbonded pdb=" OG SER B 751 " pdb=" O1 CYZ B 903 " model vdw 2.083 2.432 nonbonded pdb=" OD1 ASP B 799 " pdb=" OG SER B 802 " model vdw 2.174 3.040 nonbonded pdb=" OE1 GLU D 727 " pdb=" OH TYR D 754 " model vdw 2.222 3.040 nonbonded pdb=" O TYR B 733 " pdb=" NH1 ARG B 737 " model vdw 2.262 3.120 nonbonded pdb=" OD2 ASP D 750 " pdb=" NZ LYS D 752 " model vdw 2.264 3.120 ... (remaining 149121 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 416 through 901) selection = (chain 'B' and resid 416 through 901) selection = chain 'C' selection = (chain 'D' and resid 416 through 901) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.300 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.016 0.482 18529 Z= 0.805 Angle : 0.873 22.188 25042 Z= 0.428 Chirality : 0.122 2.131 2800 Planarity : 0.008 0.097 3056 Dihedral : 13.671 119.015 6672 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.50 % Favored : 94.10 % Rotamer: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2256 helix: -0.48 (0.13), residues: 1294 sheet: -1.54 (0.44), residues: 120 loop : -1.50 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.004 ARG B 737 TYR 0.024 0.004 TYR G 176 PHE 0.021 0.002 PHE D 836 TRP 0.027 0.002 TRP H 178 HIS 0.005 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.01616 (18516) covalent geometry : angle 0.87346 (25020) SS BOND : bond 0.00300 ( 11) SS BOND : angle 0.80688 ( 22) hydrogen bonds : bond 0.12009 ( 1064) hydrogen bonds : angle 5.89698 ( 3054) Misc. bond : bond 0.00393 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 575 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 PHE cc_start: 0.4635 (m-80) cc_final: 0.4374 (m-80) REVERT: A 667 ILE cc_start: 0.9030 (mt) cc_final: 0.8403 (mp) REVERT: A 676 SER cc_start: 0.9323 (t) cc_final: 0.8889 (m) REVERT: A 677 THR cc_start: 0.9395 (m) cc_final: 0.8961 (p) REVERT: A 730 MET cc_start: 0.8888 (mpp) cc_final: 0.8593 (mpp) REVERT: A 742 THR cc_start: 0.8559 (p) cc_final: 0.8144 (p) REVERT: A 770 LEU cc_start: 0.9177 (mm) cc_final: 0.8916 (pp) REVERT: B 436 MET cc_start: 0.9394 (ptt) cc_final: 0.8521 (tmm) REVERT: B 485 MET cc_start: 0.8723 (mtm) cc_final: 0.8500 (mtm) REVERT: B 526 ILE cc_start: 0.9553 (pt) cc_final: 0.8923 (pt) REVERT: B 607 MET cc_start: 0.9082 (mmm) cc_final: 0.8847 (mmt) REVERT: B 692 MET cc_start: 0.9342 (mtp) cc_final: 0.9112 (mmp) REVERT: B 706 ARG cc_start: 0.8968 (ttp80) cc_final: 0.8595 (ttp-110) REVERT: B 786 ASN cc_start: 0.9453 (m-40) cc_final: 0.9166 (m-40) REVERT: C 423 MET cc_start: 0.8403 (mmm) cc_final: 0.7892 (mmm) REVERT: C 446 TYR cc_start: 0.9006 (t80) cc_final: 0.8538 (t80) REVERT: C 472 TYR cc_start: 0.8116 (m-80) cc_final: 0.7688 (m-80) REVERT: C 522 ILE cc_start: 0.9128 (mt) cc_final: 0.8644 (mm) REVERT: C 525 MET cc_start: 0.8744 (ttm) cc_final: 0.8489 (ttm) REVERT: C 607 MET cc_start: 0.9094 (mmt) cc_final: 0.8707 (mmm) REVERT: C 769 ASN cc_start: 0.8534 (t0) cc_final: 0.8004 (t0) REVERT: C 773 LEU cc_start: 0.9147 (mt) cc_final: 0.8805 (mm) REVERT: D 485 MET cc_start: 0.8524 (mtm) cc_final: 0.8060 (mtm) REVERT: D 518 MET cc_start: 0.8512 (ttm) cc_final: 0.8265 (ttp) REVERT: D 661 LEU cc_start: 0.8776 (mt) cc_final: 0.8546 (mt) REVERT: H 22 SER cc_start: 0.9533 (m) cc_final: 0.9022 (t) REVERT: H 116 PHE cc_start: 0.8706 (t80) cc_final: 0.8143 (t80) REVERT: H 134 ILE cc_start: 0.8367 (mt) cc_final: 0.7922 (tp) REVERT: F 32 TYR cc_start: 0.8096 (m-80) cc_final: 0.7801 (m-80) REVERT: F 58 MET cc_start: 0.7815 (mmm) cc_final: 0.7561 (mpp) REVERT: F 64 TRP cc_start: 0.8639 (m100) cc_final: 0.8360 (m-10) REVERT: F 200 MET cc_start: 0.8893 (mtm) cc_final: 0.8363 (mtt) REVERT: G 56 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7734 (pm20) REVERT: E 106 ILE cc_start: 0.9274 (tt) cc_final: 0.9069 (tp) REVERT: E 116 PHE cc_start: 0.8937 (t80) cc_final: 0.8558 (t80) REVERT: E 117 MET cc_start: 0.8661 (mmm) cc_final: 0.8427 (mmm) REVERT: E 203 ASP cc_start: 0.9032 (t0) cc_final: 0.8831 (t0) outliers start: 2 outliers final: 0 residues processed: 576 average time/residue: 0.1536 time to fit residues: 131.2492 Evaluate side-chains 313 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN B 434 HIS ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN F 205 HIS F 207 GLN G 149 ASN E 132 HIS E 149 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.102835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072563 restraints weight = 53773.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073617 restraints weight = 27121.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073847 restraints weight = 18658.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074209 restraints weight = 18084.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074301 restraints weight = 16375.679| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 18529 Z= 0.270 Angle : 0.730 12.465 25042 Z= 0.386 Chirality : 0.046 0.187 2800 Planarity : 0.004 0.046 3056 Dihedral : 9.491 110.073 2596 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 4.16 % Allowed : 12.84 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2256 helix: 1.29 (0.14), residues: 1306 sheet: -1.72 (0.38), residues: 152 loop : -1.11 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 6 TYR 0.027 0.002 TYR C 545 PHE 0.018 0.002 PHE F 21 TRP 0.014 0.002 TRP E 33 HIS 0.007 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00610 (18516) covalent geometry : angle 0.72925 (25020) SS BOND : bond 0.00822 ( 11) SS BOND : angle 1.56190 ( 22) hydrogen bonds : bond 0.04603 ( 1064) hydrogen bonds : angle 4.72383 ( 3054) Misc. bond : bond 0.00323 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 328 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 SER cc_start: 0.9463 (t) cc_final: 0.8928 (p) REVERT: A 677 THR cc_start: 0.9362 (m) cc_final: 0.9016 (p) REVERT: A 678 LYS cc_start: 0.9273 (tttt) cc_final: 0.8866 (pttp) REVERT: A 748 ASN cc_start: 0.6922 (m-40) cc_final: 0.6610 (t0) REVERT: A 770 LEU cc_start: 0.9217 (mm) cc_final: 0.8967 (pp) REVERT: B 429 MET cc_start: 0.6008 (mpp) cc_final: 0.5558 (mpp) REVERT: B 433 ASN cc_start: 0.8999 (p0) cc_final: 0.8791 (p0) REVERT: B 436 MET cc_start: 0.9400 (ptt) cc_final: 0.8928 (ppp) REVERT: B 546 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 607 MET cc_start: 0.9197 (mmm) cc_final: 0.7883 (mmm) REVERT: B 679 GLU cc_start: 0.8857 (tp30) cc_final: 0.8524 (tp30) REVERT: B 727 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8129 (mp0) REVERT: B 743 MET cc_start: 0.9069 (ptm) cc_final: 0.8656 (ptt) REVERT: B 790 TYR cc_start: 0.7954 (m-80) cc_final: 0.7753 (m-80) REVERT: C 423 MET cc_start: 0.8225 (mmm) cc_final: 0.7724 (mmm) REVERT: C 472 TYR cc_start: 0.8355 (m-80) cc_final: 0.7852 (m-80) REVERT: C 607 MET cc_start: 0.9154 (mmt) cc_final: 0.8598 (mmm) REVERT: C 683 ARG cc_start: 0.8373 (ptm160) cc_final: 0.8147 (mtm180) REVERT: C 692 MET cc_start: 0.8789 (mmm) cc_final: 0.8508 (mmm) REVERT: C 708 THR cc_start: 0.8465 (p) cc_final: 0.8184 (t) REVERT: D 485 MET cc_start: 0.8587 (mtm) cc_final: 0.8321 (mtm) REVERT: D 635 ILE cc_start: 0.9280 (tt) cc_final: 0.8955 (tp) REVERT: D 737 ARG cc_start: 0.8700 (mmt-90) cc_final: 0.8336 (mmt-90) REVERT: D 743 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7728 (pmm) REVERT: H 70 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7619 (tm-30) REVERT: H 99 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.9084 (ttm110) REVERT: F 58 MET cc_start: 0.7611 (mmm) cc_final: 0.6882 (mpp) REVERT: F 64 TRP cc_start: 0.8974 (m100) cc_final: 0.8559 (m-10) REVERT: F 70 GLU cc_start: 0.8971 (mp0) cc_final: 0.8637 (mp0) REVERT: F 115 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8899 (mp) REVERT: G 56 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7940 (pm20) REVERT: G 64 TRP cc_start: 0.8449 (m100) cc_final: 0.8129 (m100) REVERT: G 74 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8546 (tmtt) REVERT: E 65 ARG cc_start: 0.8666 (mtp-110) cc_final: 0.8352 (mtp-110) REVERT: E 116 PHE cc_start: 0.9164 (t80) cc_final: 0.8771 (t80) REVERT: E 117 MET cc_start: 0.8859 (mmm) cc_final: 0.8536 (mmm) REVERT: E 203 ASP cc_start: 0.9349 (t0) cc_final: 0.9040 (t0) outliers start: 80 outliers final: 50 residues processed: 375 average time/residue: 0.1247 time to fit residues: 72.2488 Evaluate side-chains 320 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.073146 restraints weight = 53549.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074900 restraints weight = 33948.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075019 restraints weight = 20682.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075277 restraints weight = 19955.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075387 restraints weight = 19312.364| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18529 Z= 0.142 Angle : 0.607 7.690 25042 Z= 0.316 Chirality : 0.042 0.198 2800 Planarity : 0.004 0.062 3056 Dihedral : 8.743 108.863 2596 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 3.27 % Allowed : 14.29 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 2256 helix: 1.94 (0.15), residues: 1308 sheet: -1.52 (0.41), residues: 130 loop : -0.96 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 475 TYR 0.027 0.001 TYR C 545 PHE 0.016 0.001 PHE F 21 TRP 0.025 0.001 TRP A 693 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00322 (18516) covalent geometry : angle 0.60659 (25020) SS BOND : bond 0.00702 ( 11) SS BOND : angle 1.06323 ( 22) hydrogen bonds : bond 0.03881 ( 1064) hydrogen bonds : angle 4.14284 ( 3054) Misc. bond : bond 0.00263 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 334 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 TRP cc_start: 0.9379 (t-100) cc_final: 0.8846 (t-100) REVERT: A 651 MET cc_start: 0.6998 (mmm) cc_final: 0.6472 (mpp) REVERT: A 659 GLU cc_start: 0.9310 (mp0) cc_final: 0.8824 (pm20) REVERT: A 676 SER cc_start: 0.9455 (t) cc_final: 0.9020 (m) REVERT: A 677 THR cc_start: 0.9374 (m) cc_final: 0.9098 (p) REVERT: A 678 LYS cc_start: 0.9165 (tttt) cc_final: 0.8816 (pttp) REVERT: A 735 GLU cc_start: 0.9381 (tt0) cc_final: 0.9091 (tm-30) REVERT: A 748 ASN cc_start: 0.7174 (m-40) cc_final: 0.6816 (t0) REVERT: A 770 LEU cc_start: 0.9129 (mm) cc_final: 0.8899 (pp) REVERT: B 436 MET cc_start: 0.9326 (ptt) cc_final: 0.8842 (ppp) REVERT: B 472 TYR cc_start: 0.8765 (m-80) cc_final: 0.8437 (m-80) REVERT: B 546 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 607 MET cc_start: 0.9073 (mmm) cc_final: 0.7571 (mmm) REVERT: B 692 MET cc_start: 0.9209 (ttm) cc_final: 0.8860 (mmp) REVERT: B 743 MET cc_start: 0.9309 (ptm) cc_final: 0.8749 (ptt) REVERT: C 436 MET cc_start: 0.9036 (mmm) cc_final: 0.8757 (mpp) REVERT: C 472 TYR cc_start: 0.8223 (m-80) cc_final: 0.7717 (m-80) REVERT: C 522 ILE cc_start: 0.9276 (mp) cc_final: 0.8909 (tp) REVERT: C 607 MET cc_start: 0.9120 (mmt) cc_final: 0.8537 (mmm) REVERT: C 692 MET cc_start: 0.8823 (mmm) cc_final: 0.8575 (mmm) REVERT: C 708 THR cc_start: 0.8490 (p) cc_final: 0.8211 (t) REVERT: D 485 MET cc_start: 0.8498 (mtm) cc_final: 0.8139 (mtm) REVERT: D 518 MET cc_start: 0.8939 (ttp) cc_final: 0.8639 (ttp) REVERT: D 547 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8964 (mt) REVERT: H 70 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7763 (tm-30) REVERT: H 81 ASP cc_start: 0.8261 (t0) cc_final: 0.7979 (t0) REVERT: H 116 PHE cc_start: 0.8871 (t80) cc_final: 0.8448 (t80) REVERT: H 200 MET cc_start: 0.7983 (mtm) cc_final: 0.7626 (mmm) REVERT: F 58 MET cc_start: 0.7506 (mmm) cc_final: 0.7009 (mpp) REVERT: F 64 TRP cc_start: 0.8911 (m100) cc_final: 0.8554 (m-10) REVERT: F 70 GLU cc_start: 0.8920 (mp0) cc_final: 0.8596 (mp0) REVERT: G 25 THR cc_start: 0.9492 (t) cc_final: 0.9222 (p) REVERT: G 56 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8033 (pm20) REVERT: G 74 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8556 (tmtt) REVERT: G 149 ASN cc_start: 0.9219 (t0) cc_final: 0.8981 (t0) REVERT: E 58 MET cc_start: 0.7817 (tpp) cc_final: 0.7571 (tmm) REVERT: E 65 ARG cc_start: 0.8657 (mtp-110) cc_final: 0.8253 (mtp-110) REVERT: E 116 PHE cc_start: 0.9088 (t80) cc_final: 0.8634 (t80) REVERT: E 117 MET cc_start: 0.8690 (mmm) cc_final: 0.8404 (mmm) REVERT: E 132 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6836 (m-70) REVERT: E 174 TYR cc_start: 0.8624 (p90) cc_final: 0.8392 (p90) REVERT: E 203 ASP cc_start: 0.9334 (t0) cc_final: 0.9006 (t0) outliers start: 63 outliers final: 33 residues processed: 371 average time/residue: 0.1254 time to fit residues: 72.3165 Evaluate side-chains 319 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 736 GLN F 149 ASN F 205 HIS F 207 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.104675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074399 restraints weight = 53833.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075437 restraints weight = 27312.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075707 restraints weight = 18831.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076047 restraints weight = 18387.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076143 restraints weight = 16567.079| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18529 Z= 0.155 Angle : 0.617 13.168 25042 Z= 0.314 Chirality : 0.042 0.187 2800 Planarity : 0.004 0.049 3056 Dihedral : 8.221 109.217 2596 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 3.27 % Allowed : 16.27 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2256 helix: 2.01 (0.15), residues: 1314 sheet: -1.57 (0.40), residues: 150 loop : -0.81 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 475 TYR 0.026 0.001 TYR C 545 PHE 0.015 0.001 PHE F 21 TRP 0.022 0.001 TRP B 600 HIS 0.016 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00356 (18516) covalent geometry : angle 0.61712 (25020) SS BOND : bond 0.00410 ( 11) SS BOND : angle 0.89589 ( 22) hydrogen bonds : bond 0.03786 ( 1064) hydrogen bonds : angle 4.08768 ( 3054) Misc. bond : bond 0.00222 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 303 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 TRP cc_start: 0.9389 (t-100) cc_final: 0.8881 (t-100) REVERT: A 651 MET cc_start: 0.7212 (mmm) cc_final: 0.6749 (mpp) REVERT: A 659 GLU cc_start: 0.9332 (mp0) cc_final: 0.8789 (pm20) REVERT: A 672 LEU cc_start: 0.7377 (tt) cc_final: 0.6942 (mt) REVERT: A 676 SER cc_start: 0.9446 (t) cc_final: 0.8916 (p) REVERT: A 677 THR cc_start: 0.9349 (m) cc_final: 0.9083 (p) REVERT: A 726 LEU cc_start: 0.9002 (tp) cc_final: 0.8780 (tp) REVERT: A 730 MET cc_start: 0.9321 (mtm) cc_final: 0.8594 (pmm) REVERT: A 735 GLU cc_start: 0.9395 (tt0) cc_final: 0.9093 (tm-30) REVERT: A 748 ASN cc_start: 0.7234 (m-40) cc_final: 0.6896 (t0) REVERT: A 770 LEU cc_start: 0.9211 (mm) cc_final: 0.8940 (pp) REVERT: B 436 MET cc_start: 0.9372 (ptt) cc_final: 0.8855 (ppp) REVERT: B 472 TYR cc_start: 0.8739 (m-80) cc_final: 0.8500 (m-80) REVERT: B 498 ILE cc_start: 0.9339 (mt) cc_final: 0.8927 (tt) REVERT: B 501 LEU cc_start: 0.9290 (tp) cc_final: 0.9084 (tt) REVERT: B 546 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 679 GLU cc_start: 0.8794 (tp30) cc_final: 0.8444 (tp30) REVERT: B 743 MET cc_start: 0.9316 (ptm) cc_final: 0.8762 (ptt) REVERT: C 472 TYR cc_start: 0.8123 (m-80) cc_final: 0.7487 (m-80) REVERT: C 485 MET cc_start: 0.8256 (mtm) cc_final: 0.7419 (mtm) REVERT: C 522 ILE cc_start: 0.9294 (mp) cc_final: 0.8885 (tp) REVERT: C 607 MET cc_start: 0.9149 (mmt) cc_final: 0.8819 (mmm) REVERT: C 683 ARG cc_start: 0.8281 (mtm180) cc_final: 0.8045 (mtm110) REVERT: C 692 MET cc_start: 0.8939 (mmm) cc_final: 0.8680 (mmm) REVERT: C 708 THR cc_start: 0.8489 (p) cc_final: 0.8186 (t) REVERT: D 485 MET cc_start: 0.8532 (mtm) cc_final: 0.7722 (mtm) REVERT: D 518 MET cc_start: 0.8928 (ttp) cc_final: 0.8676 (ttp) REVERT: D 547 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8884 (mt) REVERT: D 692 MET cc_start: 0.8403 (mmp) cc_final: 0.8141 (mmm) REVERT: D 696 MET cc_start: 0.9004 (ttm) cc_final: 0.8775 (ttm) REVERT: D 743 MET cc_start: 0.8523 (pmm) cc_final: 0.8219 (pmm) REVERT: D 775 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8929 (mm) REVERT: H 81 ASP cc_start: 0.8200 (t0) cc_final: 0.7868 (t0) REVERT: H 99 ARG cc_start: 0.9254 (tpp80) cc_final: 0.9028 (ttm110) REVERT: H 116 PHE cc_start: 0.8824 (t80) cc_final: 0.8422 (t80) REVERT: H 199 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7903 (t-90) REVERT: H 200 MET cc_start: 0.7994 (mtm) cc_final: 0.7631 (mmm) REVERT: F 58 MET cc_start: 0.7466 (mmm) cc_final: 0.7027 (mpp) REVERT: F 64 TRP cc_start: 0.8982 (m100) cc_final: 0.8562 (m-10) REVERT: F 70 GLU cc_start: 0.8939 (mp0) cc_final: 0.8629 (mp0) REVERT: F 115 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8917 (mp) REVERT: G 25 THR cc_start: 0.9512 (t) cc_final: 0.9242 (p) REVERT: G 56 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8047 (pm20) REVERT: G 74 LYS cc_start: 0.9015 (mtmm) cc_final: 0.8570 (tmtt) REVERT: E 58 MET cc_start: 0.7697 (tpp) cc_final: 0.7466 (tmm) REVERT: E 65 ARG cc_start: 0.8709 (mtp-110) cc_final: 0.8292 (mtp-110) REVERT: E 116 PHE cc_start: 0.9115 (t80) cc_final: 0.8686 (t80) REVERT: E 203 ASP cc_start: 0.9347 (t0) cc_final: 0.9035 (t0) outliers start: 63 outliers final: 40 residues processed: 343 average time/residue: 0.1214 time to fit residues: 65.3716 Evaluate side-chains 318 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN F 149 ASN F 205 HIS ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.104695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072890 restraints weight = 53667.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.075197 restraints weight = 26101.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076658 restraints weight = 17380.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077374 restraints weight = 13763.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.077932 restraints weight = 12219.431| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18529 Z= 0.153 Angle : 0.601 9.183 25042 Z= 0.306 Chirality : 0.041 0.225 2800 Planarity : 0.004 0.045 3056 Dihedral : 7.648 109.000 2596 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 3.27 % Allowed : 16.79 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 2256 helix: 2.08 (0.15), residues: 1314 sheet: -1.47 (0.37), residues: 174 loop : -0.91 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 475 TYR 0.025 0.001 TYR C 545 PHE 0.018 0.001 PHE F 180 TRP 0.014 0.001 TRP B 600 HIS 0.003 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00351 (18516) covalent geometry : angle 0.60089 (25020) SS BOND : bond 0.00448 ( 11) SS BOND : angle 0.95452 ( 22) hydrogen bonds : bond 0.03681 ( 1064) hydrogen bonds : angle 4.02403 ( 3054) Misc. bond : bond 0.00197 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8813 (mt) REVERT: A 423 MET cc_start: 0.8174 (tpp) cc_final: 0.7109 (mmm) REVERT: A 429 MET cc_start: 0.8102 (mmm) cc_final: 0.7836 (mmm) REVERT: A 520 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8213 (pp) REVERT: A 600 TRP cc_start: 0.9389 (t-100) cc_final: 0.8861 (t-100) REVERT: A 651 MET cc_start: 0.7226 (mmm) cc_final: 0.6703 (mpp) REVERT: A 676 SER cc_start: 0.9481 (t) cc_final: 0.8952 (p) REVERT: A 677 THR cc_start: 0.9320 (m) cc_final: 0.9040 (p) REVERT: A 726 LEU cc_start: 0.9076 (tp) cc_final: 0.8715 (tp) REVERT: A 730 MET cc_start: 0.9395 (mtm) cc_final: 0.8627 (pmm) REVERT: A 735 GLU cc_start: 0.9369 (tt0) cc_final: 0.9087 (tm-30) REVERT: A 748 ASN cc_start: 0.7291 (m-40) cc_final: 0.6853 (t0) REVERT: A 770 LEU cc_start: 0.9211 (mm) cc_final: 0.8936 (pp) REVERT: B 436 MET cc_start: 0.9331 (ptt) cc_final: 0.8602 (ppp) REVERT: B 472 TYR cc_start: 0.8662 (m-80) cc_final: 0.8418 (m-80) REVERT: B 485 MET cc_start: 0.8936 (mmm) cc_final: 0.7965 (mmt) REVERT: B 498 ILE cc_start: 0.9341 (mt) cc_final: 0.8996 (tt) REVERT: B 546 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7846 (mt-10) REVERT: B 607 MET cc_start: 0.9044 (mmm) cc_final: 0.8493 (mmm) REVERT: B 679 GLU cc_start: 0.8813 (tp30) cc_final: 0.8459 (tp30) REVERT: B 692 MET cc_start: 0.8755 (mmp) cc_final: 0.8369 (tpp) REVERT: B 743 MET cc_start: 0.9299 (ptm) cc_final: 0.8707 (ptt) REVERT: C 472 TYR cc_start: 0.8067 (m-80) cc_final: 0.7398 (m-80) REVERT: C 485 MET cc_start: 0.8229 (mtm) cc_final: 0.7462 (mtm) REVERT: C 607 MET cc_start: 0.9119 (mmt) cc_final: 0.8633 (mmm) REVERT: C 692 MET cc_start: 0.8931 (mmm) cc_final: 0.8662 (mmm) REVERT: C 708 THR cc_start: 0.8488 (p) cc_final: 0.8175 (t) REVERT: D 485 MET cc_start: 0.8461 (mtm) cc_final: 0.8029 (mtm) REVERT: D 518 MET cc_start: 0.9044 (ttp) cc_final: 0.8752 (ttp) REVERT: D 520 LEU cc_start: 0.9208 (pp) cc_final: 0.8865 (pp) REVERT: D 737 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.8330 (mmt-90) REVERT: D 743 MET cc_start: 0.8569 (pmm) cc_final: 0.8151 (pmm) REVERT: H 81 ASP cc_start: 0.8199 (t0) cc_final: 0.7863 (t0) REVERT: H 116 PHE cc_start: 0.8812 (t80) cc_final: 0.8394 (t80) REVERT: H 199 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7936 (t-90) REVERT: H 200 MET cc_start: 0.7987 (mtm) cc_final: 0.7605 (mmm) REVERT: F 10 MET cc_start: 0.8960 (tpp) cc_final: 0.8192 (mpp) REVERT: F 18 PHE cc_start: 0.9087 (t80) cc_final: 0.8784 (t80) REVERT: F 58 MET cc_start: 0.7342 (mmm) cc_final: 0.6968 (mpp) REVERT: F 64 TRP cc_start: 0.8984 (m100) cc_final: 0.8616 (m-10) REVERT: F 115 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8933 (mp) REVERT: G 25 THR cc_start: 0.9496 (t) cc_final: 0.9256 (p) REVERT: G 56 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8163 (pm20) REVERT: G 64 TRP cc_start: 0.8413 (m100) cc_final: 0.8154 (m100) REVERT: E 65 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8316 (mtp-110) REVERT: E 116 PHE cc_start: 0.8997 (t80) cc_final: 0.8554 (t80) REVERT: E 117 MET cc_start: 0.9008 (mmm) cc_final: 0.8254 (mpp) REVERT: E 203 ASP cc_start: 0.9372 (t0) cc_final: 0.9028 (t0) outliers start: 63 outliers final: 49 residues processed: 336 average time/residue: 0.1295 time to fit residues: 68.5609 Evaluate side-chains 328 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 109 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 204 optimal weight: 7.9990 chunk 169 optimal weight: 0.0870 chunk 191 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 786 ASN H 149 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS F 207 GLN G 149 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.105412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075529 restraints weight = 53278.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076591 restraints weight = 25746.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077180 restraints weight = 17934.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077460 restraints weight = 17725.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077512 restraints weight = 15622.179| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18529 Z= 0.131 Angle : 0.601 8.843 25042 Z= 0.302 Chirality : 0.041 0.177 2800 Planarity : 0.004 0.046 3056 Dihedral : 7.219 108.647 2596 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 3.53 % Allowed : 17.57 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.19), residues: 2256 helix: 2.14 (0.15), residues: 1314 sheet: -1.46 (0.37), residues: 174 loop : -0.84 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.033 0.001 TYR D 695 PHE 0.014 0.001 PHE C 630 TRP 0.010 0.001 TRP B 600 HIS 0.002 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00299 (18516) covalent geometry : angle 0.60115 (25020) SS BOND : bond 0.00392 ( 11) SS BOND : angle 0.89049 ( 22) hydrogen bonds : bond 0.03557 ( 1064) hydrogen bonds : angle 3.96944 ( 3054) Misc. bond : bond 0.00203 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 308 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8191 (tpp) cc_final: 0.7102 (mmm) REVERT: A 429 MET cc_start: 0.8318 (mmm) cc_final: 0.8050 (mmm) REVERT: A 520 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 600 TRP cc_start: 0.9372 (t-100) cc_final: 0.8767 (t-100) REVERT: A 651 MET cc_start: 0.7296 (mmm) cc_final: 0.6790 (mpp) REVERT: A 672 LEU cc_start: 0.7302 (tt) cc_final: 0.6910 (mt) REVERT: A 676 SER cc_start: 0.9516 (t) cc_final: 0.9031 (p) REVERT: A 726 LEU cc_start: 0.9038 (tp) cc_final: 0.8694 (tp) REVERT: A 730 MET cc_start: 0.9401 (mtm) cc_final: 0.8624 (pmm) REVERT: A 735 GLU cc_start: 0.9355 (tt0) cc_final: 0.9056 (tm-30) REVERT: A 748 ASN cc_start: 0.7333 (m-40) cc_final: 0.6865 (t0) REVERT: A 770 LEU cc_start: 0.9206 (mm) cc_final: 0.8931 (pp) REVERT: B 436 MET cc_start: 0.9328 (ptt) cc_final: 0.8672 (ppp) REVERT: B 472 TYR cc_start: 0.8732 (m-80) cc_final: 0.8525 (m-80) REVERT: B 485 MET cc_start: 0.8959 (mmm) cc_final: 0.8147 (mmt) REVERT: B 498 ILE cc_start: 0.9392 (mt) cc_final: 0.9055 (tt) REVERT: B 546 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 607 MET cc_start: 0.9072 (mmm) cc_final: 0.8664 (mmm) REVERT: B 679 GLU cc_start: 0.8745 (tp30) cc_final: 0.8401 (tp30) REVERT: B 743 MET cc_start: 0.9293 (ptm) cc_final: 0.8846 (ptt) REVERT: C 472 TYR cc_start: 0.7980 (m-80) cc_final: 0.7397 (m-80) REVERT: C 485 MET cc_start: 0.8257 (mtm) cc_final: 0.7352 (mtm) REVERT: C 522 ILE cc_start: 0.9226 (mp) cc_final: 0.8874 (tp) REVERT: C 607 MET cc_start: 0.9071 (mmt) cc_final: 0.8527 (mmm) REVERT: C 672 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7747 (tp) REVERT: C 692 MET cc_start: 0.8946 (mmm) cc_final: 0.8680 (mmm) REVERT: C 708 THR cc_start: 0.8480 (p) cc_final: 0.8062 (t) REVERT: D 485 MET cc_start: 0.8411 (mtm) cc_final: 0.7879 (mtm) REVERT: D 520 LEU cc_start: 0.9186 (pp) cc_final: 0.8809 (pp) REVERT: D 541 ASP cc_start: 0.8783 (m-30) cc_final: 0.8433 (m-30) REVERT: D 737 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.8287 (mmt-90) REVERT: D 743 MET cc_start: 0.8522 (pmm) cc_final: 0.7611 (pmm) REVERT: H 81 ASP cc_start: 0.8265 (t0) cc_final: 0.7864 (t0) REVERT: H 99 ARG cc_start: 0.9312 (ttm110) cc_final: 0.8587 (mtm-85) REVERT: H 116 PHE cc_start: 0.8774 (t80) cc_final: 0.8368 (t80) REVERT: H 199 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7948 (t-90) REVERT: H 200 MET cc_start: 0.7931 (mtm) cc_final: 0.7539 (mmm) REVERT: F 18 PHE cc_start: 0.9043 (t80) cc_final: 0.8789 (t80) REVERT: F 64 TRP cc_start: 0.9003 (m100) cc_final: 0.8585 (m-10) REVERT: F 115 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8901 (mp) REVERT: G 25 THR cc_start: 0.9514 (t) cc_final: 0.9241 (p) REVERT: G 56 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8164 (pm20) REVERT: G 64 TRP cc_start: 0.8442 (m100) cc_final: 0.8164 (m100) REVERT: G 74 LYS cc_start: 0.9011 (mtmm) cc_final: 0.8636 (mmtt) REVERT: G 207 GLN cc_start: 0.6516 (tm-30) cc_final: 0.6277 (tm-30) REVERT: E 65 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8298 (mtp-110) REVERT: E 116 PHE cc_start: 0.9016 (t80) cc_final: 0.8579 (t80) REVERT: E 117 MET cc_start: 0.9027 (mmm) cc_final: 0.8303 (mpp) REVERT: E 191 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9036 (mm-30) REVERT: E 203 ASP cc_start: 0.9358 (t0) cc_final: 0.9035 (t0) outliers start: 68 outliers final: 43 residues processed: 352 average time/residue: 0.1266 time to fit residues: 70.4965 Evaluate side-chains 333 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 222 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN B 530 GLN D 609 GLN F 149 ASN F 205 HIS F 207 GLN G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.105502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075618 restraints weight = 53666.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076903 restraints weight = 25708.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077084 restraints weight = 17661.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077455 restraints weight = 17731.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077513 restraints weight = 16085.988| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18529 Z= 0.130 Angle : 0.602 9.230 25042 Z= 0.304 Chirality : 0.041 0.178 2800 Planarity : 0.004 0.044 3056 Dihedral : 6.920 108.450 2596 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 3.38 % Allowed : 18.66 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2256 helix: 2.15 (0.15), residues: 1306 sheet: -1.45 (0.38), residues: 170 loop : -0.78 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.035 0.001 TYR D 695 PHE 0.017 0.001 PHE C 630 TRP 0.008 0.001 TRP D 693 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00299 (18516) covalent geometry : angle 0.60142 (25020) SS BOND : bond 0.00359 ( 11) SS BOND : angle 0.82323 ( 22) hydrogen bonds : bond 0.03557 ( 1064) hydrogen bonds : angle 3.95101 ( 3054) Misc. bond : bond 0.00219 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 299 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8165 (tpp) cc_final: 0.7251 (mmm) REVERT: A 600 TRP cc_start: 0.9360 (t-100) cc_final: 0.8768 (t-100) REVERT: A 651 MET cc_start: 0.7380 (mmm) cc_final: 0.6896 (mpp) REVERT: A 676 SER cc_start: 0.9615 (t) cc_final: 0.9205 (p) REVERT: A 735 GLU cc_start: 0.9356 (tt0) cc_final: 0.9047 (tm-30) REVERT: A 748 ASN cc_start: 0.7362 (m-40) cc_final: 0.6908 (t0) REVERT: A 770 LEU cc_start: 0.9203 (mm) cc_final: 0.8932 (pp) REVERT: B 436 MET cc_start: 0.9295 (ptt) cc_final: 0.8698 (ppp) REVERT: B 472 TYR cc_start: 0.8760 (m-80) cc_final: 0.8493 (m-80) REVERT: B 485 MET cc_start: 0.8959 (mmm) cc_final: 0.8085 (mmt) REVERT: B 498 ILE cc_start: 0.9406 (mt) cc_final: 0.9114 (tt) REVERT: B 607 MET cc_start: 0.9000 (mmm) cc_final: 0.8686 (mmm) REVERT: B 692 MET cc_start: 0.8753 (mmp) cc_final: 0.8507 (tpp) REVERT: C 472 TYR cc_start: 0.7963 (m-80) cc_final: 0.7428 (m-80) REVERT: C 485 MET cc_start: 0.8255 (mtm) cc_final: 0.7368 (mtm) REVERT: C 522 ILE cc_start: 0.9215 (mp) cc_final: 0.8846 (tp) REVERT: C 607 MET cc_start: 0.9078 (mmt) cc_final: 0.8730 (mmm) REVERT: C 672 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7746 (tp) REVERT: C 692 MET cc_start: 0.8946 (mmm) cc_final: 0.8703 (mmm) REVERT: C 708 THR cc_start: 0.8524 (p) cc_final: 0.8146 (t) REVERT: D 429 MET cc_start: 0.8419 (mtp) cc_final: 0.8108 (mtm) REVERT: D 485 MET cc_start: 0.8366 (mtm) cc_final: 0.7856 (mtm) REVERT: D 489 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7940 (tp) REVERT: D 520 LEU cc_start: 0.9235 (pp) cc_final: 0.8925 (pp) REVERT: D 541 ASP cc_start: 0.8733 (m-30) cc_final: 0.8366 (m-30) REVERT: D 737 ARG cc_start: 0.8614 (mmt-90) cc_final: 0.7969 (mmp80) REVERT: D 743 MET cc_start: 0.8561 (pmm) cc_final: 0.7718 (pmm) REVERT: H 81 ASP cc_start: 0.8215 (t0) cc_final: 0.7830 (t0) REVERT: H 116 PHE cc_start: 0.8754 (t80) cc_final: 0.8343 (t80) REVERT: H 191 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8686 (mm-30) REVERT: H 199 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7966 (t-90) REVERT: H 200 MET cc_start: 0.7939 (mtm) cc_final: 0.7529 (mmm) REVERT: F 18 PHE cc_start: 0.9045 (t80) cc_final: 0.8801 (t80) REVERT: F 64 TRP cc_start: 0.9022 (m100) cc_final: 0.8545 (m-10) REVERT: F 115 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8883 (mp) REVERT: G 25 THR cc_start: 0.9493 (t) cc_final: 0.9244 (p) REVERT: G 56 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8154 (pm20) REVERT: G 64 TRP cc_start: 0.8467 (m100) cc_final: 0.8184 (m100) REVERT: G 74 LYS cc_start: 0.9010 (mtmm) cc_final: 0.8645 (mmtt) REVERT: G 203 ASP cc_start: 0.8921 (t0) cc_final: 0.8195 (t0) REVERT: E 65 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8153 (mtp-110) REVERT: E 116 PHE cc_start: 0.9004 (t80) cc_final: 0.8540 (t80) REVERT: E 117 MET cc_start: 0.9062 (mmm) cc_final: 0.8373 (mpp) REVERT: E 203 ASP cc_start: 0.9345 (t0) cc_final: 0.9024 (t0) outliers start: 65 outliers final: 48 residues processed: 340 average time/residue: 0.1174 time to fit residues: 63.0094 Evaluate side-chains 327 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 ASN F 205 HIS F 207 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.104453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074199 restraints weight = 53938.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075396 restraints weight = 27093.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075630 restraints weight = 18591.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076133 restraints weight = 18558.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076143 restraints weight = 16808.003| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18529 Z= 0.164 Angle : 0.626 9.464 25042 Z= 0.316 Chirality : 0.042 0.236 2800 Planarity : 0.004 0.045 3056 Dihedral : 6.738 108.593 2596 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.92 % Rotamer: Outliers : 3.53 % Allowed : 19.39 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 2256 helix: 2.14 (0.15), residues: 1306 sheet: -1.64 (0.39), residues: 152 loop : -0.80 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.037 0.001 TYR D 695 PHE 0.015 0.001 PHE C 630 TRP 0.009 0.001 TRP B 548 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00380 (18516) covalent geometry : angle 0.62580 (25020) SS BOND : bond 0.00378 ( 11) SS BOND : angle 0.87792 ( 22) hydrogen bonds : bond 0.03677 ( 1064) hydrogen bonds : angle 4.05443 ( 3054) Misc. bond : bond 0.00208 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 283 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8135 (tpp) cc_final: 0.7333 (mmm) REVERT: A 600 TRP cc_start: 0.9399 (t-100) cc_final: 0.8847 (t-100) REVERT: A 651 MET cc_start: 0.7460 (mmm) cc_final: 0.6964 (mpp) REVERT: A 676 SER cc_start: 0.9612 (t) cc_final: 0.9181 (p) REVERT: A 735 GLU cc_start: 0.9365 (tt0) cc_final: 0.9047 (tm-30) REVERT: A 770 LEU cc_start: 0.9221 (mm) cc_final: 0.8947 (pp) REVERT: B 436 MET cc_start: 0.9351 (ptt) cc_final: 0.8678 (ppp) REVERT: B 472 TYR cc_start: 0.8757 (m-80) cc_final: 0.8409 (m-80) REVERT: B 485 MET cc_start: 0.8986 (mmm) cc_final: 0.8107 (mmt) REVERT: B 498 ILE cc_start: 0.9411 (mt) cc_final: 0.9128 (tt) REVERT: B 546 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 607 MET cc_start: 0.9035 (mmm) cc_final: 0.8725 (mmm) REVERT: B 679 GLU cc_start: 0.8726 (tp30) cc_final: 0.8280 (tp30) REVERT: B 692 MET cc_start: 0.8779 (mmp) cc_final: 0.8578 (tpp) REVERT: C 472 TYR cc_start: 0.8028 (m-80) cc_final: 0.7367 (m-80) REVERT: C 485 MET cc_start: 0.8269 (mtm) cc_final: 0.7386 (mtm) REVERT: C 522 ILE cc_start: 0.9251 (mp) cc_final: 0.8869 (tp) REVERT: C 607 MET cc_start: 0.9094 (mmt) cc_final: 0.8550 (mmm) REVERT: C 672 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7734 (tp) REVERT: C 692 MET cc_start: 0.9002 (mmm) cc_final: 0.8718 (mmm) REVERT: C 708 THR cc_start: 0.8514 (p) cc_final: 0.8123 (t) REVERT: D 429 MET cc_start: 0.8393 (mtp) cc_final: 0.8169 (mtm) REVERT: D 485 MET cc_start: 0.8370 (mtm) cc_final: 0.7885 (mtm) REVERT: D 520 LEU cc_start: 0.9251 (pp) cc_final: 0.8944 (pp) REVERT: D 541 ASP cc_start: 0.8742 (m-30) cc_final: 0.8367 (m-30) REVERT: D 737 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.8018 (mmp80) REVERT: D 743 MET cc_start: 0.8660 (pmm) cc_final: 0.7859 (pmm) REVERT: H 81 ASP cc_start: 0.8185 (t0) cc_final: 0.7779 (t0) REVERT: H 99 ARG cc_start: 0.9340 (ttm110) cc_final: 0.8596 (mtm-85) REVERT: H 116 PHE cc_start: 0.8785 (t80) cc_final: 0.8366 (t80) REVERT: H 191 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8761 (mm-30) REVERT: H 199 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7954 (t-90) REVERT: H 200 MET cc_start: 0.7958 (mtm) cc_final: 0.7535 (mmm) REVERT: F 18 PHE cc_start: 0.9046 (t80) cc_final: 0.8815 (t80) REVERT: F 64 TRP cc_start: 0.9094 (m100) cc_final: 0.8607 (m-10) REVERT: F 115 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8877 (mp) REVERT: G 25 THR cc_start: 0.9508 (t) cc_final: 0.9268 (p) REVERT: G 56 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8154 (pm20) REVERT: G 64 TRP cc_start: 0.8508 (m100) cc_final: 0.8204 (m100) REVERT: G 74 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8365 (tptm) REVERT: E 65 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8142 (mtp-110) REVERT: E 116 PHE cc_start: 0.9007 (t80) cc_final: 0.8565 (t80) REVERT: E 117 MET cc_start: 0.9063 (mmm) cc_final: 0.8379 (mpp) REVERT: E 191 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8950 (mm-30) REVERT: E 203 ASP cc_start: 0.9359 (t0) cc_final: 0.9057 (t0) outliers start: 68 outliers final: 56 residues processed: 324 average time/residue: 0.1145 time to fit residues: 59.1701 Evaluate side-chains 331 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 205 HIS F 207 GLN G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.105895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074577 restraints weight = 53264.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076859 restraints weight = 26520.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078270 restraints weight = 17770.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079086 restraints weight = 14182.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079437 restraints weight = 12531.176| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18529 Z= 0.122 Angle : 0.620 12.679 25042 Z= 0.309 Chirality : 0.041 0.243 2800 Planarity : 0.004 0.071 3056 Dihedral : 6.491 108.241 2596 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 3.33 % Allowed : 19.85 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2256 helix: 2.26 (0.15), residues: 1292 sheet: -1.26 (0.39), residues: 156 loop : -0.87 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 99 TYR 0.039 0.001 TYR D 695 PHE 0.019 0.001 PHE B 724 TRP 0.010 0.001 TRP B 600 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00279 (18516) covalent geometry : angle 0.61967 (25020) SS BOND : bond 0.00336 ( 11) SS BOND : angle 0.83629 ( 22) hydrogen bonds : bond 0.03521 ( 1064) hydrogen bonds : angle 3.96026 ( 3054) Misc. bond : bond 0.00193 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 297 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8187 (tpp) cc_final: 0.7449 (mmm) REVERT: A 600 TRP cc_start: 0.9338 (t-100) cc_final: 0.8729 (t-100) REVERT: A 607 MET cc_start: 0.8856 (mmt) cc_final: 0.8212 (mmm) REVERT: A 651 MET cc_start: 0.7365 (mmm) cc_final: 0.7038 (mpp) REVERT: A 672 LEU cc_start: 0.7587 (mt) cc_final: 0.6723 (tt) REVERT: A 676 SER cc_start: 0.9613 (t) cc_final: 0.9221 (p) REVERT: A 735 GLU cc_start: 0.9338 (tt0) cc_final: 0.9050 (tm-30) REVERT: A 770 LEU cc_start: 0.9215 (mm) cc_final: 0.8941 (pp) REVERT: B 436 MET cc_start: 0.9294 (ptt) cc_final: 0.8627 (ppp) REVERT: B 472 TYR cc_start: 0.8805 (m-80) cc_final: 0.8495 (m-80) REVERT: B 485 MET cc_start: 0.8961 (mmm) cc_final: 0.8041 (mmt) REVERT: B 498 ILE cc_start: 0.9396 (mt) cc_final: 0.9115 (tt) REVERT: B 503 ILE cc_start: 0.8859 (mp) cc_final: 0.8566 (mp) REVERT: B 546 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 679 GLU cc_start: 0.8691 (tp30) cc_final: 0.8234 (tp30) REVERT: C 472 TYR cc_start: 0.7940 (m-80) cc_final: 0.7272 (m-80) REVERT: C 485 MET cc_start: 0.8223 (mtm) cc_final: 0.7103 (mtm) REVERT: C 522 ILE cc_start: 0.9240 (mp) cc_final: 0.8854 (tp) REVERT: C 607 MET cc_start: 0.9068 (mmt) cc_final: 0.8716 (mmm) REVERT: C 672 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7697 (tp) REVERT: C 692 MET cc_start: 0.8937 (mmm) cc_final: 0.8695 (mmm) REVERT: C 708 THR cc_start: 0.8601 (p) cc_final: 0.8229 (t) REVERT: D 482 TRP cc_start: 0.7161 (m100) cc_final: 0.6818 (m100) REVERT: D 485 MET cc_start: 0.8320 (mtm) cc_final: 0.7812 (mtm) REVERT: D 489 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8051 (tp) REVERT: D 520 LEU cc_start: 0.9153 (pp) cc_final: 0.8827 (pp) REVERT: D 541 ASP cc_start: 0.8736 (m-30) cc_final: 0.8350 (m-30) REVERT: D 737 ARG cc_start: 0.8672 (mmt-90) cc_final: 0.8038 (mmp80) REVERT: D 743 MET cc_start: 0.8621 (pmm) cc_final: 0.7803 (pmm) REVERT: D 810 SER cc_start: 0.9139 (t) cc_final: 0.8800 (p) REVERT: H 81 ASP cc_start: 0.8162 (t0) cc_final: 0.7810 (t0) REVERT: H 99 ARG cc_start: 0.9320 (ttm110) cc_final: 0.8619 (mtm-85) REVERT: H 116 PHE cc_start: 0.8761 (t80) cc_final: 0.8335 (t80) REVERT: H 191 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8702 (mm-30) REVERT: H 199 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7986 (t-90) REVERT: H 200 MET cc_start: 0.7931 (mtm) cc_final: 0.7512 (mmm) REVERT: F 18 PHE cc_start: 0.8952 (t80) cc_final: 0.8718 (t80) REVERT: F 64 TRP cc_start: 0.9019 (m100) cc_final: 0.8565 (m-10) REVERT: F 115 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8910 (mp) REVERT: G 25 THR cc_start: 0.9481 (t) cc_final: 0.9250 (p) REVERT: G 56 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8182 (pm20) REVERT: G 64 TRP cc_start: 0.8416 (m100) cc_final: 0.8124 (m100) REVERT: G 74 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8599 (mmtt) REVERT: E 65 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8168 (mtp-110) REVERT: E 116 PHE cc_start: 0.8954 (t80) cc_final: 0.8481 (t80) REVERT: E 117 MET cc_start: 0.9023 (mmm) cc_final: 0.8350 (mpp) REVERT: E 191 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8860 (mm-30) REVERT: E 203 ASP cc_start: 0.9368 (t0) cc_final: 0.9051 (t0) outliers start: 64 outliers final: 48 residues processed: 337 average time/residue: 0.1191 time to fit residues: 63.8145 Evaluate side-chains 333 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN C 608 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS F 207 GLN G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.104812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073307 restraints weight = 53680.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075557 restraints weight = 26777.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076914 restraints weight = 17970.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077701 restraints weight = 14410.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078080 restraints weight = 12757.769| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18529 Z= 0.166 Angle : 0.648 11.014 25042 Z= 0.326 Chirality : 0.042 0.222 2800 Planarity : 0.004 0.113 3056 Dihedral : 6.488 108.475 2596 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 3.33 % Allowed : 20.53 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 2256 helix: 2.17 (0.15), residues: 1294 sheet: -1.73 (0.40), residues: 156 loop : -0.75 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG E 99 TYR 0.040 0.001 TYR D 695 PHE 0.015 0.001 PHE C 630 TRP 0.009 0.001 TRP B 548 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00386 (18516) covalent geometry : angle 0.64745 (25020) SS BOND : bond 0.00344 ( 11) SS BOND : angle 1.06199 ( 22) hydrogen bonds : bond 0.03703 ( 1064) hydrogen bonds : angle 4.09231 ( 3054) Misc. bond : bond 0.00202 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 278 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8118 (tpp) cc_final: 0.7423 (mmm) REVERT: A 600 TRP cc_start: 0.9381 (t-100) cc_final: 0.8833 (t-100) REVERT: A 651 MET cc_start: 0.7395 (mmm) cc_final: 0.7077 (mpp) REVERT: A 676 SER cc_start: 0.9609 (t) cc_final: 0.9206 (p) REVERT: A 677 THR cc_start: 0.9329 (m) cc_final: 0.9101 (m) REVERT: A 726 LEU cc_start: 0.8816 (tt) cc_final: 0.8614 (tt) REVERT: A 735 GLU cc_start: 0.9336 (tt0) cc_final: 0.9082 (tm-30) REVERT: A 770 LEU cc_start: 0.9222 (mm) cc_final: 0.8946 (pp) REVERT: B 436 MET cc_start: 0.9300 (ptt) cc_final: 0.8633 (ppp) REVERT: B 472 TYR cc_start: 0.8754 (m-80) cc_final: 0.8408 (m-80) REVERT: B 485 MET cc_start: 0.8977 (mmm) cc_final: 0.8034 (mmt) REVERT: B 498 ILE cc_start: 0.9389 (mt) cc_final: 0.9094 (tt) REVERT: B 503 ILE cc_start: 0.8838 (mp) cc_final: 0.8533 (mp) REVERT: B 546 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 651 MET cc_start: 0.7782 (tpp) cc_final: 0.7575 (tpp) REVERT: B 679 GLU cc_start: 0.8704 (tp30) cc_final: 0.8262 (tp30) REVERT: C 472 TYR cc_start: 0.7992 (m-80) cc_final: 0.7334 (m-80) REVERT: C 485 MET cc_start: 0.8229 (mtm) cc_final: 0.7313 (mtm) REVERT: C 522 ILE cc_start: 0.9240 (mp) cc_final: 0.8855 (tp) REVERT: C 607 MET cc_start: 0.9060 (mmt) cc_final: 0.8507 (mmm) REVERT: C 672 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7714 (tp) REVERT: C 692 MET cc_start: 0.8924 (mmm) cc_final: 0.8677 (mmm) REVERT: C 708 THR cc_start: 0.8571 (p) cc_final: 0.8195 (t) REVERT: D 485 MET cc_start: 0.8320 (mtm) cc_final: 0.7809 (mtm) REVERT: D 489 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8067 (tp) REVERT: D 541 ASP cc_start: 0.8707 (m-30) cc_final: 0.8332 (m-30) REVERT: D 737 ARG cc_start: 0.8683 (mmt-90) cc_final: 0.8050 (mmp80) REVERT: D 743 MET cc_start: 0.8673 (pmm) cc_final: 0.7894 (pmm) REVERT: D 810 SER cc_start: 0.9150 (t) cc_final: 0.8828 (p) REVERT: H 81 ASP cc_start: 0.8148 (t0) cc_final: 0.7793 (t0) REVERT: H 99 ARG cc_start: 0.9328 (ttm110) cc_final: 0.8632 (mtm-85) REVERT: H 116 PHE cc_start: 0.8776 (t80) cc_final: 0.8338 (t80) REVERT: H 191 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8777 (mm-30) REVERT: H 199 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7984 (t-90) REVERT: H 200 MET cc_start: 0.7967 (mtm) cc_final: 0.7563 (mmm) REVERT: F 18 PHE cc_start: 0.8949 (t80) cc_final: 0.8727 (t80) REVERT: F 64 TRP cc_start: 0.9100 (m100) cc_final: 0.8599 (m-10) REVERT: F 115 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8899 (mp) REVERT: G 25 THR cc_start: 0.9488 (t) cc_final: 0.9264 (p) REVERT: G 56 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8181 (pm20) REVERT: G 64 TRP cc_start: 0.8465 (m100) cc_final: 0.8181 (m100) REVERT: G 74 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8304 (tptm) REVERT: E 65 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8151 (mtp-110) REVERT: E 116 PHE cc_start: 0.8961 (t80) cc_final: 0.8498 (t80) REVERT: E 117 MET cc_start: 0.9039 (mmm) cc_final: 0.8376 (mpp) REVERT: E 191 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8862 (mm-30) REVERT: E 203 ASP cc_start: 0.9380 (t0) cc_final: 0.9063 (t0) outliers start: 64 outliers final: 53 residues processed: 317 average time/residue: 0.1144 time to fit residues: 58.5940 Evaluate side-chains 333 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 213 optimal weight: 6.9990 chunk 165 optimal weight: 0.1980 chunk 172 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 211 optimal weight: 0.0040 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS F 207 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.107288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076128 restraints weight = 53302.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078449 restraints weight = 26168.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079906 restraints weight = 17423.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080790 restraints weight = 13819.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081094 restraints weight = 12109.782| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18529 Z= 0.118 Angle : 0.638 10.823 25042 Z= 0.315 Chirality : 0.042 0.313 2800 Planarity : 0.004 0.080 3056 Dihedral : 6.343 108.190 2596 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 2.55 % Allowed : 21.26 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2256 helix: 2.20 (0.15), residues: 1288 sheet: -1.48 (0.35), residues: 196 loop : -0.83 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 99 TYR 0.038 0.001 TYR D 695 PHE 0.020 0.001 PHE C 630 TRP 0.012 0.001 TRP A 628 HIS 0.003 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00261 (18516) covalent geometry : angle 0.63781 (25020) SS BOND : bond 0.00312 ( 11) SS BOND : angle 1.00171 ( 22) hydrogen bonds : bond 0.03492 ( 1064) hydrogen bonds : angle 3.96461 ( 3054) Misc. bond : bond 0.00179 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.35 seconds wall clock time: 54 minutes 39.41 seconds (3279.41 seconds total)