Starting phenix.real_space_refine on Thu Mar 5 03:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9g_71410/03_2026/9p9g_71410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9g_71410/03_2026/9p9g_71410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9g_71410/03_2026/9p9g_71410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9g_71410/03_2026/9p9g_71410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9g_71410/03_2026/9p9g_71410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9g_71410/03_2026/9p9g_71410.map" } resolution = 4.06 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18100 Number of models: 1 Model: "" Number of chains: 14 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': 1, 'PTRANS': 14, '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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CYZ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Time building chain proxies: 3.60, per 1000 atoms: 0.20 Number of scatterers: 18100 At special positions: 0 Unit cell: (130.2, 111.6, 134.85, 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=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.02 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 776.6 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: 100 helices and 22 sheets defined 59.6% alpha, 9.0% 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 432 through 435 removed outlier: 4.382A pdb=" N GLU A 435 " --> pdb=" O LYS A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.546A pdb=" N LYS A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 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 removed outlier: 4.539A pdb=" N TRP A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 Processing helix chain 'A' and resid 617 through 646 removed outlier: 3.614A pdb=" N VAL A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.782A pdb=" N GLU A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.528A pdb=" N ARG A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 779 through 791 Processing helix chain 'A' and resid 798 through 802 removed outlier: 4.082A pdb=" N GLY A 801 " --> pdb=" O LYS A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 840 removed outlier: 3.726A pdb=" N VAL A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.783A 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 537 through 541 Processing helix chain 'B' and resid 544 through 568 Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 617 through 640 Processing helix chain 'B' and resid 641 through 646 removed outlier: 3.736A pdb=" N PHE B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 675 through 683 Processing helix chain 'B' and resid 686 through 697 Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 728 through 737 Processing helix chain 'B' and resid 764 through 779 Processing helix chain 'B' and resid 779 through 789 removed outlier: 3.837A pdb=" N LYS B 783 " --> pdb=" O GLY B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 Processing helix chain 'B' and resid 814 through 840 removed outlier: 3.978A 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 removed outlier: 3.640A pdb=" N TYR C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) 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 537 through 541 Processing helix chain 'C' and resid 544 through 568 Processing helix chain 'C' and resid 594 through 607 Processing helix chain 'C' and resid 617 through 646 removed outlier: 3.602A pdb=" N ALA C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 645 " --> pdb=" O ASN C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 675 through 684 removed outlier: 3.721A pdb=" N GLU C 679 " --> pdb=" O GLY C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 699 Processing helix chain 'C' and resid 707 through 719 Processing helix chain 'C' and resid 728 through 736 removed outlier: 4.037A pdb=" N GLN C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 778 Processing helix chain 'C' and resid 779 through 789 Processing helix chain 'C' and resid 790 through 793 Processing helix chain 'C' and resid 810 through 814 Processing helix chain 'C' and resid 815 through 839 removed outlier: 4.410A pdb=" N LYS C 839 " --> pdb=" O GLU C 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 removed outlier: 4.478A pdb=" N GLU D 435 " --> pdb=" O LYS D 432 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 544 through 568 Processing helix chain 'D' and resid 594 through 607 Processing helix chain 'D' and resid 617 through 640 Processing helix chain 'D' and resid 657 through 664 removed outlier: 3.584A pdb=" N LEU D 661 " --> pdb=" O SER D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 682 Processing helix chain 'D' and resid 686 through 699 Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 728 through 736 removed outlier: 3.550A pdb=" N GLN D 736 " --> pdb=" O GLU D 732 " (cutoff:3.500A) 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: 3.558A 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 840 removed outlier: 3.515A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU D 830 " --> pdb=" O GLY D 826 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 29 removed outlier: 4.263A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 74 removed outlier: 4.033A pdb=" N PHE H 73 " --> pdb=" O GLU H 70 " (cutoff:3.500A) 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: 3.664A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 29 removed outlier: 3.955A pdb=" N LEU F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 125 Processing helix chain 'F' and resid 132 through 160 Processing helix chain 'F' and resid 177 through 208 removed outlier: 3.648A pdb=" N PHE F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 210 No H-bonds generated for 'chain 'F' and resid 209 through 210' Processing helix chain 'G' and resid 6 through 7 No H-bonds generated for 'chain 'G' and resid 6 through 7' Processing helix chain 'G' and resid 8 through 29 removed outlier: 3.514A 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 210 removed outlier: 3.595A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 209 " --> pdb=" O HIS G 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 29 removed outlier: 3.745A pdb=" N LEU E 11 " --> pdb=" O GLY E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 105 through 124 removed outlier: 3.596A pdb=" N ILE E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 159 removed outlier: 3.610A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 207 removed outlier: 3.510A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 466 removed outlier: 5.801A pdb=" N VAL A 417 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA A 465 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL A 419 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 496 " --> pdb=" O VAL A 418 " (cutoff:3.500A) 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 520 removed outlier: 4.909A pdb=" N VAL A 756 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A 754 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET A 518 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS A 752 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 704 through 705 removed outlier: 8.464A pdb=" N THR A 705 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR A 671 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N LEU A 672 " --> pdb=" O GLU A 727 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 462 through 466 removed outlier: 6.275A pdb=" N VAL B 417 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 465 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 419 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA7, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AA9, first strand: chain 'B' and resid 704 through 705 removed outlier: 8.609A pdb=" N THR B 705 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 671 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 725 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 670 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N GLU B 727 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N LEU B 672 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N PHE B 722 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYS B 527 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB2, first strand: chain 'C' and resid 462 through 466 Processing sheet with id=AB3, first strand: chain 'C' and resid 511 through 520 removed outlier: 5.056A pdb=" N VAL C 756 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR C 754 " --> pdb=" O PRO C 516 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET C 518 " --> pdb=" O LYS C 752 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS C 752 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 704 through 705 removed outlier: 9.350A pdb=" N THR C 705 " --> pdb=" O TYR C 669 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR C 671 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N LEU C 672 " --> pdb=" O GLU C 727 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 462 through 466 Processing sheet with id=AB6, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AB7, first strand: chain 'D' and resid 512 through 513 Processing sheet with id=AB8, first strand: chain 'D' and resid 518 through 520 removed outlier: 3.667A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 704 through 705 removed outlier: 8.116A pdb=" N THR D 705 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR D 671 " --> pdb=" O THR D 705 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU D 725 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N LEU D 672 " --> pdb=" O GLU D 727 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N PHE D 722 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS D 527 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.529A pdb=" N MET F 58 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AC4, first strand: chain 'E' and resid 77 through 79 1067 hydrogen bonds defined for protein. 3063 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: 1.91 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: 5548 1.36 - 1.52: 10429 1.52 - 1.69: 2303 1.69 - 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 902 " pdb=" C5 CYZ B 902 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.80e+02 bond pdb=" C4 CYZ B 903 " pdb=" C5 CYZ B 903 " ideal model delta sigma weight residual 1.512 1.032 0.480 2.00e-02 2.50e+03 5.77e+02 bond pdb=" C4 CYZ A 903 " pdb=" C5 CYZ A 903 " ideal model delta sigma weight residual 1.512 1.033 0.479 2.00e-02 2.50e+03 5.74e+02 bond pdb=" C1 CYZ A 902 " pdb=" C2 CYZ A 902 " ideal model delta sigma weight residual 1.557 1.079 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: 24876 4.44 - 8.88: 117 8.88 - 13.32: 11 13.32 - 17.76: 11 17.76 - 22.21: 5 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 106.92 129.13 -22.21 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C1 CYZ A 903 " pdb=" C2 CYZ A 903 " pdb=" C3 CYZ A 903 " ideal model delta sigma weight residual 106.92 128.24 -21.32 3.00e+00 1.11e-01 5.05e+01 angle pdb=" C1 CYZ B 902 " pdb=" C2 CYZ B 902 " pdb=" C3 CYZ B 902 " ideal model delta sigma weight residual 106.92 128.08 -21.16 3.00e+00 1.11e-01 4.97e+01 angle pdb=" C1 CYZ A 902 " pdb=" C2 CYZ A 902 " pdb=" C3 CYZ A 902 " ideal model delta sigma weight residual 106.92 127.84 -20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" O3 CYZ B 902 " pdb=" S2 CYZ B 902 " pdb=" O4 CYZ B 902 " ideal model delta sigma weight residual 118.35 100.01 18.34 3.00e+00 1.11e-01 3.74e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 10554 26.70 - 53.40: 294 53.40 - 80.10: 36 80.10 - 106.80: 18 106.80 - 133.50: 8 Dihedral angle restraints: 10910 sinusoidal: 4314 harmonic: 6596 Sorted by residual: dihedral pdb=" CA ASP F 81 " pdb=" C ASP F 81 " pdb=" N HIS F 82 " pdb=" CA HIS F 82 " 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 ASP H 81 " pdb=" C ASP H 81 " pdb=" N HIS H 82 " pdb=" CA HIS H 82 " ideal model delta harmonic sigma weight residual -180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ASP G 81 " pdb=" C ASP G 81 " pdb=" N HIS G 82 " pdb=" CA HIS G 82 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 10907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.427: 2788 0.427 - 0.855: 4 0.855 - 1.282: 0 1.282 - 1.710: 0 1.710 - 2.137: 8 Chirality restraints: 2800 Sorted by residual: 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 1.17 2.14 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" C5 CYZ A 903 " pdb=" C4 CYZ A 903 " pdb=" C6 CYZ A 903 " pdb=" C7 CYZ A 903 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.14 2.00e-01 2.50e+01 1.14e+02 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 2.14 2.00e-01 2.50e+01 1.14e+02 ... (remaining 2797 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 516 " -0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C PRO B 516 " 0.092 2.00e-02 2.50e+03 pdb=" O PRO B 516 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE B 517 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 472 " 0.008 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR A 472 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 472 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 472 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 472 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR A 472 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 472 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR A 472 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 CYZ B 902 " -0.037 2.00e-02 2.50e+03 2.20e-02 1.20e+01 pdb=" C11 CYZ B 902 " 0.041 2.00e-02 2.50e+03 pdb=" C12 CYZ B 902 " -0.002 2.00e-02 2.50e+03 pdb=" C13 CYZ B 902 " -0.003 2.00e-02 2.50e+03 pdb=" C14 CYZ B 902 " -0.001 2.00e-02 2.50e+03 pdb=" C9 CYZ B 902 " -0.020 2.00e-02 2.50e+03 pdb=" N2 CYZ B 902 " 0.035 2.00e-02 2.50e+03 pdb=" S1 CYZ B 902 " -0.011 2.00e-02 2.50e+03 pdb=" S2 CYZ B 902 " -0.001 2.00e-02 2.50e+03 pdb="CL CYZ B 902 " -0.001 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 352 2.65 - 3.22: 19254 3.22 - 3.78: 29891 3.78 - 4.34: 39479 4.34 - 4.90: 62914 Nonbonded interactions: 151890 Sorted by model distance: nonbonded pdb=" O GLY G 38 " pdb=" OG1 THR G 59 " model vdw 2.092 3.040 nonbonded pdb=" OE1 GLU A 727 " pdb=" OH TYR A 754 " model vdw 2.120 3.040 nonbonded pdb=" OE1 GLU C 727 " pdb=" OH TYR C 754 " model vdw 2.140 3.040 nonbonded pdb=" OE1 GLU D 727 " pdb=" OH TYR D 754 " model vdw 2.143 3.040 nonbonded pdb=" OG SER D 519 " pdb=" O2 CYZ A 903 " model vdw 2.183 3.040 ... (remaining 151885 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: 0.01 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' } 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.180 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 : 0.017 0.482 18532 Z= 0.830 Angle : 0.957 22.205 25040 Z= 0.468 Chirality : 0.121 2.137 2800 Planarity : 0.008 0.115 3056 Dihedral : 14.147 133.503 6672 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.36 % Favored : 94.06 % Rotamer: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.60 (0.16), residues: 2256 helix: -0.49 (0.13), residues: 1263 sheet: -1.71 (0.39), residues: 155 loop : -1.65 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG C 765 TYR 0.042 0.005 TYR A 472 PHE 0.056 0.003 PHE A 568 TRP 0.035 0.003 TRP B 789 HIS 0.007 0.002 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.01668 (18516) covalent geometry : angle 0.95716 (25020) SS BOND : bond 0.00432 ( 10) SS BOND : angle 1.27607 ( 20) hydrogen bonds : bond 0.13383 ( 1067) hydrogen bonds : angle 6.14645 ( 3063) Misc. bond : bond 0.00975 ( 6) *********************** 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 735 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 732 time to evaluate : 0.781 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 ILE cc_start: 0.8655 (mt) cc_final: 0.7659 (mt) REVERT: A 525 MET cc_start: 0.8236 (ttm) cc_final: 0.7919 (mtp) REVERT: A 629 PHE cc_start: 0.8813 (t80) cc_final: 0.8597 (t80) REVERT: A 641 ASN cc_start: 0.9109 (t0) cc_final: 0.8412 (t0) REVERT: A 681 PHE cc_start: 0.8288 (m-80) cc_final: 0.7291 (m-80) REVERT: A 695 TYR cc_start: 0.8651 (t80) cc_final: 0.8365 (t80) REVERT: A 704 PHE cc_start: 0.8286 (m-80) cc_final: 0.7929 (m-80) REVERT: A 748 ASN cc_start: 0.6185 (m-40) cc_final: 0.5845 (m-40) REVERT: A 752 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7427 (mmtt) REVERT: B 534 PRO cc_start: 0.6839 (Cg_exo) cc_final: 0.5632 (Cg_endo) REVERT: B 696 MET cc_start: 0.8105 (mtm) cc_final: 0.6483 (mtp) REVERT: B 715 VAL cc_start: 0.8463 (t) cc_final: 0.7897 (t) REVERT: B 724 PHE cc_start: 0.7280 (t80) cc_final: 0.7020 (t80) REVERT: B 782 ASP cc_start: 0.9034 (m-30) cc_final: 0.8651 (m-30) REVERT: B 785 LYS cc_start: 0.9477 (tttp) cc_final: 0.9108 (tptp) REVERT: B 790 TYR cc_start: 0.7376 (m-80) cc_final: 0.7043 (m-80) REVERT: C 500 PRO cc_start: 0.7579 (Cg_endo) cc_final: 0.6926 (Cg_exo) REVERT: C 608 GLN cc_start: 0.8632 (tt0) cc_final: 0.8322 (tm-30) REVERT: C 754 TYR cc_start: 0.5539 (m-10) cc_final: 0.3658 (m-10) REVERT: D 530 GLN cc_start: 0.8287 (mt0) cc_final: 0.7762 (pm20) REVERT: D 737 ARG cc_start: 0.8038 (mmp-170) cc_final: 0.7423 (mmm160) REVERT: D 765 ARG cc_start: 0.7127 (ttm170) cc_final: 0.6641 (ttt-90) REVERT: D 785 LYS cc_start: 0.9365 (tttt) cc_final: 0.9026 (ttpp) REVERT: D 786 ASN cc_start: 0.9213 (m-40) cc_final: 0.8727 (m110) REVERT: H 22 SER cc_start: 0.9303 (m) cc_final: 0.9055 (t) REVERT: H 81 ASP cc_start: 0.9232 (t0) cc_final: 0.9007 (t0) REVERT: H 108 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8738 (Cg_endo) REVERT: H 150 ILE cc_start: 0.8572 (mt) cc_final: 0.8191 (mt) REVERT: F 10 MET cc_start: 0.8019 (tpp) cc_final: 0.7460 (tmm) REVERT: F 134 ILE cc_start: 0.8257 (mt) cc_final: 0.6921 (mt) REVERT: F 153 ILE cc_start: 0.9504 (mt) cc_final: 0.9299 (mm) REVERT: G 11 LEU cc_start: 0.8624 (mp) cc_final: 0.8424 (mm) REVERT: G 58 MET cc_start: 0.8375 (mmm) cc_final: 0.7854 (tpp) REVERT: G 150 ILE cc_start: 0.8655 (mt) cc_final: 0.8245 (mt) REVERT: E 32 TYR cc_start: 0.8106 (m-80) cc_final: 0.7773 (m-80) REVERT: E 33 TRP cc_start: 0.7992 (m100) cc_final: 0.7734 (m-10) REVERT: E 120 LEU cc_start: 0.8443 (mt) cc_final: 0.8237 (mt) REVERT: E 149 ASN cc_start: 0.8925 (t0) cc_final: 0.8578 (t0) REVERT: E 204 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.7824 (mmt-90) outliers start: 3 outliers final: 0 residues processed: 735 average time/residue: 0.1515 time to fit residues: 161.5637 Evaluate side-chains 377 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 4.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN B 530 GLN C 483 ASN C 769 ASN ** D 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN H 149 ASN H 160 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS G 207 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.117642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081888 restraints weight = 51003.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083928 restraints weight = 31013.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085243 restraints weight = 22790.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085837 restraints weight = 18892.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.086451 restraints weight = 17073.393| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 18532 Z= 0.302 Angle : 0.849 12.735 25040 Z= 0.442 Chirality : 0.048 0.227 2800 Planarity : 0.006 0.054 3056 Dihedral : 9.844 114.099 2596 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.28 % Rotamer: Outliers : 0.36 % Allowed : 5.25 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.02 (0.17), residues: 2256 helix: 1.10 (0.14), residues: 1308 sheet: -1.18 (0.46), residues: 134 loop : -1.55 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 716 TYR 0.040 0.002 TYR C 472 PHE 0.024 0.002 PHE B 681 TRP 0.016 0.002 TRP D 628 HIS 0.009 0.002 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00675 (18516) covalent geometry : angle 0.84807 (25020) SS BOND : bond 0.00931 ( 10) SS BOND : angle 1.73943 ( 20) hydrogen bonds : bond 0.04850 ( 1067) hydrogen bonds : angle 4.96497 ( 3063) Misc. bond : bond 0.00643 ( 6) *********************** 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 441 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 434 time to evaluate : 0.585 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: A 422 ILE cc_start: 0.8359 (pt) cc_final: 0.8051 (mp) REVERT: A 483 ASN cc_start: 0.8007 (t0) cc_final: 0.7781 (t0) REVERT: A 748 ASN cc_start: 0.7558 (m-40) cc_final: 0.7136 (t0) REVERT: A 795 CYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5769 (t) REVERT: B 458 ILE cc_start: 0.7828 (mt) cc_final: 0.7547 (mm) REVERT: B 530 GLN cc_start: 0.6727 (tp-100) cc_final: 0.6144 (mt0) REVERT: B 786 ASN cc_start: 0.9396 (t0) cc_final: 0.9113 (t0) REVERT: C 500 PRO cc_start: 0.8263 (Cg_endo) cc_final: 0.7806 (Cg_exo) REVERT: C 531 LYS cc_start: 0.7324 (mptt) cc_final: 0.6968 (tmtt) REVERT: C 541 ASP cc_start: 0.8717 (m-30) cc_final: 0.8488 (m-30) REVERT: C 683 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.7734 (ptt90) REVERT: C 726 LEU cc_start: 0.8855 (pt) cc_final: 0.8521 (pt) REVERT: D 457 HIS cc_start: 0.8464 (m90) cc_final: 0.8239 (m90) REVERT: D 512 ASP cc_start: 0.6966 (m-30) cc_final: 0.6590 (m-30) REVERT: D 525 MET cc_start: 0.9175 (tmm) cc_final: 0.8765 (tmm) REVERT: D 667 ILE cc_start: 0.8737 (mt) cc_final: 0.8485 (mm) REVERT: D 737 ARG cc_start: 0.8033 (mmp-170) cc_final: 0.7176 (mmm160) REVERT: D 743 MET cc_start: 0.8287 (ptm) cc_final: 0.8037 (ptm) REVERT: D 769 ASN cc_start: 0.8389 (m-40) cc_final: 0.7958 (m-40) REVERT: D 786 ASN cc_start: 0.8849 (m-40) cc_final: 0.8453 (m-40) REVERT: F 11 LEU cc_start: 0.9048 (pp) cc_final: 0.8772 (mm) REVERT: F 65 ARG cc_start: 0.8332 (ttt180) cc_final: 0.8002 (ttm170) REVERT: F 192 MET cc_start: 0.8710 (mmp) cc_final: 0.7761 (tmm) REVERT: G 58 MET cc_start: 0.8802 (mmm) cc_final: 0.7897 (tpp) REVERT: G 59 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.7865 (m) REVERT: G 149 ASN cc_start: 0.9392 (t0) cc_final: 0.9189 (t0) REVERT: E 126 GLU cc_start: 0.6271 (pm20) cc_final: 0.5985 (pm20) REVERT: E 191 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8729 (mm-30) REVERT: E 204 ARG cc_start: 0.8554 (ttp-170) cc_final: 0.8022 (mmt180) outliers start: 7 outliers final: 2 residues processed: 441 average time/residue: 0.1461 time to fit residues: 94.5910 Evaluate side-chains 288 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 284 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN ** D 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.115216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.085669 restraints weight = 53873.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086603 restraints weight = 47402.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086807 restraints weight = 47791.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087189 restraints weight = 32249.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087721 restraints weight = 29162.199| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 18532 Z= 0.243 Angle : 0.703 15.104 25040 Z= 0.367 Chirality : 0.045 0.242 2800 Planarity : 0.005 0.045 3056 Dihedral : 9.310 116.439 2596 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 0.31 % Allowed : 3.95 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.53 (0.18), residues: 2256 helix: 1.60 (0.15), residues: 1307 sheet: -1.30 (0.41), residues: 168 loop : -1.44 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 204 TYR 0.022 0.002 TYR C 838 PHE 0.026 0.002 PHE A 645 TRP 0.020 0.002 TRP B 600 HIS 0.006 0.002 HIS G 199 Details of bonding type rmsd covalent geometry : bond 0.00556 (18516) covalent geometry : angle 0.70103 (25020) SS BOND : bond 0.01015 ( 10) SS BOND : angle 1.78201 ( 20) hydrogen bonds : bond 0.04266 ( 1067) hydrogen bonds : angle 4.54608 ( 3063) Misc. bond : bond 0.00619 ( 6) *********************** 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 394 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 388 time to evaluate : 0.594 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: A 607 MET cc_start: 0.8996 (mmm) cc_final: 0.8470 (mtt) REVERT: A 748 ASN cc_start: 0.7624 (m-40) cc_final: 0.7382 (t0) REVERT: A 770 LEU cc_start: 0.8346 (mp) cc_final: 0.7993 (pp) REVERT: B 496 ILE cc_start: 0.7713 (mt) cc_final: 0.7504 (mm) REVERT: B 525 MET cc_start: 0.8448 (tmm) cc_final: 0.8112 (tmm) REVERT: B 540 LEU cc_start: 0.9338 (mt) cc_final: 0.9067 (mt) REVERT: B 607 MET cc_start: 0.9364 (mmt) cc_final: 0.8765 (mmm) REVERT: B 692 MET cc_start: 0.9036 (tmm) cc_final: 0.8812 (tmm) REVERT: B 772 VAL cc_start: 0.9066 (t) cc_final: 0.8814 (p) REVERT: B 810 SER cc_start: 0.8800 (p) cc_final: 0.8461 (p) REVERT: C 436 MET cc_start: 0.9212 (mmp) cc_final: 0.9003 (mmp) REVERT: C 607 MET cc_start: 0.9241 (mmm) cc_final: 0.8644 (mmm) REVERT: C 683 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.7850 (ptt90) REVERT: C 726 LEU cc_start: 0.8526 (pt) cc_final: 0.8255 (tp) REVERT: C 743 MET cc_start: 0.8433 (ptt) cc_final: 0.8162 (ptm) REVERT: C 819 TYR cc_start: 0.9275 (m-10) cc_final: 0.8997 (m-80) REVERT: D 447 CYS cc_start: 0.7866 (m) cc_final: 0.7622 (m) REVERT: D 450 LEU cc_start: 0.9131 (tp) cc_final: 0.8918 (tp) REVERT: D 525 MET cc_start: 0.9005 (tmm) cc_final: 0.8738 (tmm) REVERT: D 697 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8136 (mtp85) REVERT: D 769 ASN cc_start: 0.8498 (m-40) cc_final: 0.8111 (m-40) REVERT: D 774 LYS cc_start: 0.8884 (ptpt) cc_final: 0.8576 (ptpp) REVERT: D 786 ASN cc_start: 0.8724 (m-40) cc_final: 0.8415 (m-40) REVERT: H 99 ARG cc_start: 0.8941 (mtm-85) cc_final: 0.8611 (mtm-85) REVERT: H 185 LEU cc_start: 0.9560 (tp) cc_final: 0.9309 (tt) REVERT: F 58 MET cc_start: 0.8107 (mmm) cc_final: 0.7578 (mmt) REVERT: G 185 LEU cc_start: 0.9505 (tp) cc_final: 0.9303 (tt) REVERT: E 99 ARG cc_start: 0.8231 (mtm110) cc_final: 0.8016 (mtm180) REVERT: E 113 ILE cc_start: 0.9518 (mt) cc_final: 0.9177 (mt) REVERT: E 117 MET cc_start: 0.8816 (mtm) cc_final: 0.8459 (mpp) REVERT: E 176 TYR cc_start: 0.8957 (m-80) cc_final: 0.8534 (m-80) REVERT: E 191 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8884 (mm-30) outliers start: 6 outliers final: 2 residues processed: 392 average time/residue: 0.1346 time to fit residues: 79.2090 Evaluate side-chains 287 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 HIS ** D 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.112332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.078403 restraints weight = 53281.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.080672 restraints weight = 29814.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082056 restraints weight = 21318.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082917 restraints weight = 17550.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083292 restraints weight = 15698.445| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18532 Z= 0.222 Angle : 0.655 10.337 25040 Z= 0.343 Chirality : 0.043 0.222 2800 Planarity : 0.004 0.046 3056 Dihedral : 8.791 113.442 2596 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.62 (0.18), residues: 2256 helix: 1.71 (0.15), residues: 1306 sheet: -1.32 (0.42), residues: 155 loop : -1.45 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 737 TYR 0.034 0.002 TYR A 472 PHE 0.027 0.002 PHE A 517 TRP 0.015 0.002 TRP B 693 HIS 0.010 0.002 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00511 (18516) covalent geometry : angle 0.65362 (25020) SS BOND : bond 0.00475 ( 10) SS BOND : angle 1.42645 ( 20) hydrogen bonds : bond 0.04087 ( 1067) hydrogen bonds : angle 4.45065 ( 3063) Misc. bond : bond 0.00516 ( 6) *********************** 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 379 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 375 time to evaluate : 0.660 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 525 MET cc_start: 0.8693 (ttm) cc_final: 0.8172 (ptt) REVERT: A 607 MET cc_start: 0.9077 (mmm) cc_final: 0.8332 (mmm) REVERT: A 730 MET cc_start: 0.9110 (mmt) cc_final: 0.8385 (mpp) REVERT: A 748 ASN cc_start: 0.7883 (m-40) cc_final: 0.7584 (t0) REVERT: A 770 LEU cc_start: 0.8771 (mp) cc_final: 0.8418 (pp) REVERT: B 428 VAL cc_start: 0.9277 (t) cc_final: 0.9032 (t) REVERT: B 447 CYS cc_start: 0.9053 (m) cc_final: 0.8447 (t) REVERT: B 525 MET cc_start: 0.8497 (tmm) cc_final: 0.8105 (tmm) REVERT: B 540 LEU cc_start: 0.9257 (mt) cc_final: 0.8974 (mt) REVERT: B 607 MET cc_start: 0.9387 (mmt) cc_final: 0.8857 (mmm) REVERT: B 692 MET cc_start: 0.9114 (tmm) cc_final: 0.8240 (tmm) REVERT: B 696 MET cc_start: 0.7623 (mmm) cc_final: 0.7110 (mmm) REVERT: B 748 ASN cc_start: 0.8220 (t0) cc_final: 0.7897 (t0) REVERT: B 810 SER cc_start: 0.8914 (p) cc_final: 0.8639 (p) REVERT: C 433 ASN cc_start: 0.8288 (p0) cc_final: 0.7988 (p0) REVERT: C 607 MET cc_start: 0.9212 (mmm) cc_final: 0.8591 (mmm) REVERT: C 726 LEU cc_start: 0.8811 (pt) cc_final: 0.8602 (tp) REVERT: C 730 MET cc_start: 0.9059 (mmt) cc_final: 0.8802 (mmp) REVERT: C 743 MET cc_start: 0.8607 (ptt) cc_final: 0.8302 (ptm) REVERT: C 819 TYR cc_start: 0.9290 (m-10) cc_final: 0.9058 (m-80) REVERT: D 525 MET cc_start: 0.9196 (tmm) cc_final: 0.8824 (tmm) REVERT: D 696 MET cc_start: 0.8492 (tpt) cc_final: 0.8146 (tpp) REVERT: D 743 MET cc_start: 0.8319 (ptm) cc_final: 0.8056 (ptm) REVERT: D 769 ASN cc_start: 0.8717 (m-40) cc_final: 0.8348 (m-40) REVERT: D 774 LYS cc_start: 0.9023 (ptpt) cc_final: 0.8624 (ptpp) REVERT: D 786 ASN cc_start: 0.8820 (m-40) cc_final: 0.8469 (m-40) REVERT: H 99 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8444 (mtm-85) REVERT: H 192 MET cc_start: 0.7811 (mmt) cc_final: 0.7457 (mmt) REVERT: F 58 MET cc_start: 0.8336 (mmm) cc_final: 0.7789 (mmm) REVERT: F 207 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8629 (mm-40) REVERT: G 185 LEU cc_start: 0.9473 (tp) cc_final: 0.9212 (tt) REVERT: E 21 PHE cc_start: 0.8894 (t80) cc_final: 0.8569 (t80) REVERT: E 58 MET cc_start: 0.7784 (tmm) cc_final: 0.7570 (tmm) REVERT: E 113 ILE cc_start: 0.9581 (mt) cc_final: 0.9150 (mt) REVERT: E 117 MET cc_start: 0.8893 (mtm) cc_final: 0.8402 (mpp) REVERT: E 176 TYR cc_start: 0.8992 (m-80) cc_final: 0.8727 (m-80) REVERT: E 191 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8657 (mm-30) outliers start: 4 outliers final: 2 residues processed: 378 average time/residue: 0.1355 time to fit residues: 78.0141 Evaluate side-chains 273 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 165 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 chunk 199 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS G 160 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.115639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.086392 restraints weight = 52477.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086531 restraints weight = 39205.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087141 restraints weight = 37689.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.087462 restraints weight = 26848.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087895 restraints weight = 24897.304| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18532 Z= 0.123 Angle : 0.593 7.310 25040 Z= 0.303 Chirality : 0.042 0.195 2800 Planarity : 0.004 0.047 3056 Dihedral : 8.316 115.147 2596 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.99 (0.18), residues: 2256 helix: 2.01 (0.15), residues: 1299 sheet: -1.32 (0.54), residues: 100 loop : -1.27 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 706 TYR 0.020 0.001 TYR C 472 PHE 0.026 0.001 PHE A 517 TRP 0.022 0.001 TRP D 482 HIS 0.003 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00269 (18516) covalent geometry : angle 0.59176 (25020) SS BOND : bond 0.00517 ( 10) SS BOND : angle 1.21776 ( 20) hydrogen bonds : bond 0.03566 ( 1067) hydrogen bonds : angle 4.13240 ( 3063) Misc. bond : bond 0.00511 ( 6) *********************** 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 424 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.720 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 429 MET cc_start: 0.7009 (mpp) cc_final: 0.6607 (mpp) REVERT: A 600 TRP cc_start: 0.9580 (t-100) cc_final: 0.9210 (t-100) REVERT: B 429 MET cc_start: 0.7356 (pmm) cc_final: 0.6885 (pmm) REVERT: B 436 MET cc_start: 0.7900 (pmm) cc_final: 0.7563 (pmm) REVERT: B 447 CYS cc_start: 0.8978 (m) cc_final: 0.8340 (t) REVERT: B 502 THR cc_start: 0.9312 (m) cc_final: 0.8980 (p) REVERT: B 525 MET cc_start: 0.8415 (tmm) cc_final: 0.8174 (tmm) REVERT: B 598 SER cc_start: 0.9355 (t) cc_final: 0.9106 (t) REVERT: B 607 MET cc_start: 0.9265 (mmt) cc_final: 0.8671 (mmm) REVERT: B 679 GLU cc_start: 0.8453 (tp30) cc_final: 0.8251 (tp30) REVERT: B 772 VAL cc_start: 0.9059 (t) cc_final: 0.8854 (p) REVERT: B 786 ASN cc_start: 0.9258 (t0) cc_final: 0.9003 (m110) REVERT: C 607 MET cc_start: 0.9272 (mmm) cc_final: 0.8430 (mmm) REVERT: C 726 LEU cc_start: 0.8809 (pt) cc_final: 0.8299 (tp) REVERT: C 730 MET cc_start: 0.8925 (mmt) cc_final: 0.8676 (mmp) REVERT: D 525 MET cc_start: 0.9027 (tmm) cc_final: 0.8578 (tmm) REVERT: D 696 MET cc_start: 0.8395 (tpt) cc_final: 0.8118 (tpp) REVERT: D 697 ARG cc_start: 0.8547 (mtp85) cc_final: 0.8169 (mtp85) REVERT: D 706 ARG cc_start: 0.8109 (mpt180) cc_final: 0.7856 (mmt-90) REVERT: D 765 ARG cc_start: 0.7333 (ttt-90) cc_final: 0.7004 (ttt-90) REVERT: D 769 ASN cc_start: 0.8524 (m-40) cc_final: 0.7890 (m-40) REVERT: D 774 LYS cc_start: 0.8888 (ptpt) cc_final: 0.8408 (ptpp) REVERT: D 786 ASN cc_start: 0.8840 (m-40) cc_final: 0.8406 (m-40) REVERT: H 99 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8394 (mtm-85) REVERT: F 10 MET cc_start: 0.7948 (tmm) cc_final: 0.7692 (tmm) REVERT: F 18 PHE cc_start: 0.8837 (t80) cc_final: 0.8527 (t80) REVERT: F 58 MET cc_start: 0.8118 (mmm) cc_final: 0.7888 (mmt) REVERT: G 34 LEU cc_start: 0.8778 (tp) cc_final: 0.8549 (tt) REVERT: E 58 MET cc_start: 0.7802 (tmm) cc_final: 0.7544 (tmm) REVERT: E 110 LEU cc_start: 0.9284 (tt) cc_final: 0.9081 (tt) REVERT: E 113 ILE cc_start: 0.9550 (mt) cc_final: 0.9133 (mt) REVERT: E 117 MET cc_start: 0.8820 (mtm) cc_final: 0.8532 (mpp) REVERT: E 191 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8557 (mm-30) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.1346 time to fit residues: 85.9768 Evaluate side-chains 279 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 109 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 chunk 204 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 149 ASN G 160 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084307 restraints weight = 52571.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085207 restraints weight = 37751.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085525 restraints weight = 34180.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085921 restraints weight = 25602.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086077 restraints weight = 23693.287| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.8609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18532 Z= 0.146 Angle : 0.600 7.486 25040 Z= 0.307 Chirality : 0.042 0.219 2800 Planarity : 0.004 0.048 3056 Dihedral : 8.011 114.746 2596 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.55 % Favored : 96.32 % Rotamer: Outliers : 0.10 % Allowed : 2.08 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.96 (0.19), residues: 2256 helix: 1.98 (0.15), residues: 1297 sheet: -1.41 (0.44), residues: 148 loop : -1.22 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 737 TYR 0.019 0.001 TYR B 545 PHE 0.023 0.001 PHE A 517 TRP 0.011 0.001 TRP C 789 HIS 0.006 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00334 (18516) covalent geometry : angle 0.59930 (25020) SS BOND : bond 0.00492 ( 10) SS BOND : angle 1.13209 ( 20) hydrogen bonds : bond 0.03586 ( 1067) hydrogen bonds : angle 4.13783 ( 3063) Misc. bond : bond 0.00514 ( 6) *********************** 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 382 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.654 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 525 MET cc_start: 0.8135 (ptt) cc_final: 0.7565 (ptp) REVERT: A 607 MET cc_start: 0.9044 (mmm) cc_final: 0.8273 (mmm) REVERT: A 730 MET cc_start: 0.8782 (mpp) cc_final: 0.8254 (mpp) REVERT: B 429 MET cc_start: 0.7519 (pmm) cc_final: 0.7004 (pmm) REVERT: B 447 CYS cc_start: 0.8999 (m) cc_final: 0.8438 (t) REVERT: B 502 THR cc_start: 0.9152 (m) cc_final: 0.8906 (p) REVERT: B 525 MET cc_start: 0.8460 (tmm) cc_final: 0.8252 (tmm) REVERT: B 598 SER cc_start: 0.9326 (t) cc_final: 0.9062 (t) REVERT: B 607 MET cc_start: 0.9082 (mmt) cc_final: 0.8413 (mmm) REVERT: B 692 MET cc_start: 0.8831 (tmm) cc_final: 0.7950 (tmm) REVERT: B 786 ASN cc_start: 0.9404 (t0) cc_final: 0.9113 (m110) REVERT: B 810 SER cc_start: 0.8931 (p) cc_final: 0.8574 (p) REVERT: C 485 MET cc_start: 0.6920 (tpp) cc_final: 0.6644 (tpp) REVERT: C 522 ILE cc_start: 0.9476 (mm) cc_final: 0.8895 (mm) REVERT: C 607 MET cc_start: 0.9366 (mmm) cc_final: 0.8242 (mmm) REVERT: C 726 LEU cc_start: 0.8761 (pt) cc_final: 0.8344 (tp) REVERT: C 819 TYR cc_start: 0.9288 (m-10) cc_final: 0.9014 (m-80) REVERT: D 485 MET cc_start: 0.7147 (mpp) cc_final: 0.6802 (mpp) REVERT: D 525 MET cc_start: 0.9066 (tmm) cc_final: 0.8670 (tmm) REVERT: D 696 MET cc_start: 0.8562 (tpt) cc_final: 0.8293 (tpp) REVERT: D 769 ASN cc_start: 0.8680 (m-40) cc_final: 0.8278 (m-40) REVERT: D 770 LEU cc_start: 0.8749 (pp) cc_final: 0.8495 (pp) REVERT: D 773 LEU cc_start: 0.9054 (mt) cc_final: 0.8836 (mt) REVERT: D 774 LYS cc_start: 0.8896 (ptpt) cc_final: 0.8471 (ptpp) REVERT: D 786 ASN cc_start: 0.8869 (m-40) cc_final: 0.8468 (m-40) REVERT: H 99 ARG cc_start: 0.8979 (mtm-85) cc_final: 0.8482 (mtm-85) REVERT: H 192 MET cc_start: 0.7896 (mmt) cc_final: 0.7610 (mmt) REVERT: F 10 MET cc_start: 0.8060 (tmm) cc_final: 0.7753 (tmm) REVERT: F 18 PHE cc_start: 0.9014 (t80) cc_final: 0.8661 (t80) REVERT: F 192 MET cc_start: 0.8490 (mmp) cc_final: 0.7918 (tmm) REVERT: E 58 MET cc_start: 0.7895 (tmm) cc_final: 0.7584 (tmm) REVERT: E 110 LEU cc_start: 0.9313 (tt) cc_final: 0.9076 (tt) REVERT: E 113 ILE cc_start: 0.9609 (mt) cc_final: 0.9148 (mt) REVERT: E 117 MET cc_start: 0.8959 (mtm) cc_final: 0.8577 (mpp) REVERT: E 191 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8639 (mm-30) outliers start: 2 outliers final: 0 residues processed: 380 average time/residue: 0.1282 time to fit residues: 75.4877 Evaluate side-chains 274 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN D 434 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 149 ASN G 160 ASN ** E 9 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.112936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083219 restraints weight = 53253.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083855 restraints weight = 39880.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084211 restraints weight = 36874.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084584 restraints weight = 27448.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084744 restraints weight = 25506.604| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.8954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18532 Z= 0.159 Angle : 0.604 6.520 25040 Z= 0.311 Chirality : 0.042 0.204 2800 Planarity : 0.004 0.047 3056 Dihedral : 7.858 114.889 2596 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 2256 helix: 1.88 (0.15), residues: 1297 sheet: -1.41 (0.43), residues: 150 loop : -1.18 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 737 TYR 0.022 0.001 TYR C 838 PHE 0.020 0.001 PHE A 517 TRP 0.045 0.001 TRP C 789 HIS 0.004 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00364 (18516) covalent geometry : angle 0.60380 (25020) SS BOND : bond 0.00489 ( 10) SS BOND : angle 1.07332 ( 20) hydrogen bonds : bond 0.03654 ( 1067) hydrogen bonds : angle 4.18776 ( 3063) Misc. bond : bond 0.00500 ( 6) *********************** 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 373 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.507 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 429 MET cc_start: 0.7261 (mpp) cc_final: 0.7015 (mpp) REVERT: A 600 TRP cc_start: 0.9425 (t-100) cc_final: 0.8964 (t-100) REVERT: A 730 MET cc_start: 0.8718 (mpp) cc_final: 0.8268 (mpp) REVERT: B 429 MET cc_start: 0.7578 (pmm) cc_final: 0.6974 (pmm) REVERT: B 436 MET cc_start: 0.7852 (pmm) cc_final: 0.7385 (pmm) REVERT: B 447 CYS cc_start: 0.9053 (m) cc_final: 0.8346 (t) REVERT: B 502 THR cc_start: 0.9073 (m) cc_final: 0.8865 (p) REVERT: B 598 SER cc_start: 0.9312 (t) cc_final: 0.9039 (t) REVERT: B 607 MET cc_start: 0.9154 (mmt) cc_final: 0.8576 (mmm) REVERT: B 692 MET cc_start: 0.8704 (tmm) cc_final: 0.8193 (tmm) REVERT: B 696 MET cc_start: 0.7439 (mmm) cc_final: 0.6954 (mmt) REVERT: B 786 ASN cc_start: 0.9341 (t0) cc_final: 0.9064 (m110) REVERT: C 607 MET cc_start: 0.9257 (mmm) cc_final: 0.8305 (mmm) REVERT: C 726 LEU cc_start: 0.8628 (pt) cc_final: 0.8142 (tp) REVERT: C 786 ASN cc_start: 0.9255 (m-40) cc_final: 0.9043 (m-40) REVERT: C 792 LYS cc_start: 0.5811 (ptmm) cc_final: 0.5575 (mttt) REVERT: C 819 TYR cc_start: 0.9239 (m-10) cc_final: 0.8930 (m-80) REVERT: D 482 TRP cc_start: 0.6027 (m100) cc_final: 0.5696 (m100) REVERT: D 485 MET cc_start: 0.6995 (mpp) cc_final: 0.6622 (mtm) REVERT: D 525 MET cc_start: 0.9030 (tmm) cc_final: 0.8704 (tmm) REVERT: D 769 ASN cc_start: 0.8632 (m-40) cc_final: 0.8252 (m-40) REVERT: D 774 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8465 (ptpp) REVERT: D 786 ASN cc_start: 0.8848 (m-40) cc_final: 0.8467 (m-40) REVERT: F 10 MET cc_start: 0.8039 (tmm) cc_final: 0.7751 (tmm) REVERT: F 18 PHE cc_start: 0.8948 (t80) cc_final: 0.8595 (t80) REVERT: F 24 MET cc_start: 0.8816 (tpp) cc_final: 0.8527 (tpt) REVERT: F 117 MET cc_start: 0.8880 (ttp) cc_final: 0.8436 (tmm) REVERT: F 174 TYR cc_start: 0.8131 (p90) cc_final: 0.7856 (p90) REVERT: F 192 MET cc_start: 0.8503 (mmp) cc_final: 0.8073 (tmm) REVERT: E 110 LEU cc_start: 0.9276 (tt) cc_final: 0.9057 (tt) REVERT: E 113 ILE cc_start: 0.9564 (mt) cc_final: 0.9121 (mt) REVERT: E 191 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8531 (mm-30) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.1276 time to fit residues: 73.3306 Evaluate side-chains 278 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 78 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN C 609 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 199 HIS ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 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 = 0.3830 r_free = 0.3830 target = 0.114345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084454 restraints weight = 53262.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085106 restraints weight = 37367.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085484 restraints weight = 37278.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085938 restraints weight = 27465.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086566 restraints weight = 25063.889| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.9206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18532 Z= 0.128 Angle : 0.594 9.720 25040 Z= 0.304 Chirality : 0.041 0.205 2800 Planarity : 0.004 0.046 3056 Dihedral : 7.630 115.489 2596 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.10 % Allowed : 0.88 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 2256 helix: 1.93 (0.15), residues: 1295 sheet: -1.14 (0.47), residues: 128 loop : -1.16 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 697 TYR 0.028 0.001 TYR B 545 PHE 0.018 0.001 PHE A 517 TRP 0.024 0.001 TRP C 789 HIS 0.006 0.001 HIS G 199 Details of bonding type rmsd covalent geometry : bond 0.00281 (18516) covalent geometry : angle 0.59309 (25020) SS BOND : bond 0.00533 ( 10) SS BOND : angle 1.32823 ( 20) hydrogen bonds : bond 0.03465 ( 1067) hydrogen bonds : angle 4.09493 ( 3063) Misc. bond : bond 0.00522 ( 6) *********************** 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 390 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 388 time to evaluate : 0.711 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: A 429 MET cc_start: 0.7332 (mpp) cc_final: 0.7039 (mpp) REVERT: A 600 TRP cc_start: 0.9453 (t-100) cc_final: 0.9029 (t-100) REVERT: A 607 MET cc_start: 0.9000 (mmm) cc_final: 0.8344 (mmm) REVERT: A 730 MET cc_start: 0.8733 (mpp) cc_final: 0.8258 (mpp) REVERT: B 429 MET cc_start: 0.7377 (pmm) cc_final: 0.6777 (pmm) REVERT: B 436 MET cc_start: 0.7957 (pmm) cc_final: 0.7576 (pmm) REVERT: B 447 CYS cc_start: 0.9006 (m) cc_final: 0.8345 (t) REVERT: B 598 SER cc_start: 0.9274 (t) cc_final: 0.9008 (t) REVERT: B 607 MET cc_start: 0.9138 (mmt) cc_final: 0.8539 (mmm) REVERT: B 692 MET cc_start: 0.8731 (tmm) cc_final: 0.8082 (tmm) REVERT: B 696 MET cc_start: 0.7478 (mmm) cc_final: 0.6947 (mmm) REVERT: B 786 ASN cc_start: 0.9370 (t0) cc_final: 0.9086 (m110) REVERT: C 518 MET cc_start: 0.8676 (ptp) cc_final: 0.7924 (ptp) REVERT: C 607 MET cc_start: 0.9250 (mmm) cc_final: 0.8239 (mmm) REVERT: C 786 ASN cc_start: 0.9146 (m-40) cc_final: 0.8918 (m-40) REVERT: D 485 MET cc_start: 0.7050 (mpp) cc_final: 0.6702 (mtm) REVERT: D 525 MET cc_start: 0.9052 (tmm) cc_final: 0.8653 (tmm) REVERT: D 769 ASN cc_start: 0.8588 (m-40) cc_final: 0.8182 (m-40) REVERT: D 774 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8462 (ptpp) REVERT: D 786 ASN cc_start: 0.8830 (m-40) cc_final: 0.8473 (m-40) REVERT: H 192 MET cc_start: 0.7822 (mmt) cc_final: 0.7619 (mmt) REVERT: F 10 MET cc_start: 0.8146 (tmm) cc_final: 0.7800 (tmm) REVERT: F 18 PHE cc_start: 0.8968 (t80) cc_final: 0.8622 (t80) REVERT: F 24 MET cc_start: 0.8866 (tpp) cc_final: 0.8568 (tpt) REVERT: F 174 TYR cc_start: 0.8048 (p90) cc_final: 0.7647 (p90) REVERT: E 113 ILE cc_start: 0.9563 (mt) cc_final: 0.9250 (mt) REVERT: E 117 MET cc_start: 0.8848 (mpp) cc_final: 0.8378 (mpp) REVERT: E 191 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8552 (mm-30) outliers start: 2 outliers final: 0 residues processed: 388 average time/residue: 0.1283 time to fit residues: 76.6025 Evaluate side-chains 272 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN H 160 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN G 160 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.113868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.084492 restraints weight = 53030.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.084858 restraints weight = 38853.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085586 restraints weight = 36539.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.085687 restraints weight = 27565.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086288 restraints weight = 25272.058| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.9407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18532 Z= 0.133 Angle : 0.602 8.534 25040 Z= 0.306 Chirality : 0.042 0.197 2800 Planarity : 0.004 0.046 3056 Dihedral : 7.538 115.666 2596 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 2256 helix: 1.93 (0.15), residues: 1297 sheet: -1.47 (0.41), residues: 150 loop : -1.06 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 697 TYR 0.020 0.001 TYR A 695 PHE 0.019 0.001 PHE E 180 TRP 0.023 0.001 TRP C 789 HIS 0.005 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00301 (18516) covalent geometry : angle 0.60100 (25020) SS BOND : bond 0.00433 ( 10) SS BOND : angle 1.19826 ( 20) hydrogen bonds : bond 0.03460 ( 1067) hydrogen bonds : angle 4.10442 ( 3063) Misc. bond : bond 0.00480 ( 6) *********************** 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 366 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 0.543 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: A 429 MET cc_start: 0.7465 (mpp) cc_final: 0.7171 (mpp) REVERT: A 568 PHE cc_start: 0.8143 (t80) cc_final: 0.7918 (t80) REVERT: A 600 TRP cc_start: 0.9451 (t-100) cc_final: 0.9010 (t-100) REVERT: A 607 MET cc_start: 0.9074 (mmm) cc_final: 0.8370 (mmm) REVERT: A 730 MET cc_start: 0.8787 (mpp) cc_final: 0.8314 (mpp) REVERT: A 743 MET cc_start: 0.8858 (ptm) cc_final: 0.8656 (ptm) REVERT: B 429 MET cc_start: 0.7503 (pmm) cc_final: 0.6884 (pmm) REVERT: B 436 MET cc_start: 0.8057 (pmm) cc_final: 0.7804 (pmm) REVERT: B 447 CYS cc_start: 0.9130 (m) cc_final: 0.8303 (t) REVERT: B 539 PHE cc_start: 0.9080 (p90) cc_final: 0.8847 (p90) REVERT: B 598 SER cc_start: 0.9365 (t) cc_final: 0.9075 (t) REVERT: B 607 MET cc_start: 0.9042 (mmt) cc_final: 0.8362 (mmm) REVERT: B 692 MET cc_start: 0.8763 (tmm) cc_final: 0.8129 (tmm) REVERT: B 696 MET cc_start: 0.7578 (mmm) cc_final: 0.7044 (mmm) REVERT: B 786 ASN cc_start: 0.9434 (t0) cc_final: 0.9172 (t0) REVERT: C 485 MET cc_start: 0.7523 (mtp) cc_final: 0.7110 (mtp) REVERT: C 518 MET cc_start: 0.8750 (ptp) cc_final: 0.7962 (ptp) REVERT: C 607 MET cc_start: 0.9373 (mmm) cc_final: 0.8055 (mmm) REVERT: C 819 TYR cc_start: 0.9286 (m-10) cc_final: 0.9037 (m-80) REVERT: D 485 MET cc_start: 0.7145 (mpp) cc_final: 0.6922 (mtm) REVERT: D 525 MET cc_start: 0.9095 (tmm) cc_final: 0.8663 (tmm) REVERT: D 774 LYS cc_start: 0.9005 (ptpt) cc_final: 0.8456 (ptpp) REVERT: D 786 ASN cc_start: 0.8904 (m-40) cc_final: 0.8555 (m-40) REVERT: H 192 MET cc_start: 0.7861 (mmt) cc_final: 0.7657 (mmt) REVERT: F 10 MET cc_start: 0.8188 (tmm) cc_final: 0.7784 (tmm) REVERT: F 18 PHE cc_start: 0.9018 (t80) cc_final: 0.8674 (t80) REVERT: F 24 MET cc_start: 0.8920 (tpp) cc_final: 0.8566 (tpt) REVERT: F 117 MET cc_start: 0.8906 (ttp) cc_final: 0.8654 (ttp) REVERT: F 174 TYR cc_start: 0.8301 (p90) cc_final: 0.7846 (p90) REVERT: F 176 TYR cc_start: 0.8075 (m-80) cc_final: 0.7842 (m-80) REVERT: E 113 ILE cc_start: 0.9571 (mt) cc_final: 0.9237 (mt) REVERT: E 117 MET cc_start: 0.8834 (mpp) cc_final: 0.8328 (mpp) REVERT: E 191 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8633 (mm-30) outliers start: 2 outliers final: 0 residues processed: 364 average time/residue: 0.1232 time to fit residues: 69.3217 Evaluate side-chains 271 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 201 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 213 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN C 609 GLN C 736 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 149 ASN G 160 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.111400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082129 restraints weight = 53355.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081712 restraints weight = 44872.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082374 restraints weight = 37531.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082691 restraints weight = 30905.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084784 restraints weight = 28623.703| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.9713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18532 Z= 0.178 Angle : 0.652 8.673 25040 Z= 0.333 Chirality : 0.042 0.184 2800 Planarity : 0.004 0.055 3056 Dihedral : 7.553 115.273 2596 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.96 (0.19), residues: 2256 helix: 1.93 (0.15), residues: 1293 sheet: -1.35 (0.40), residues: 164 loop : -1.10 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 697 TYR 0.024 0.001 TYR B 545 PHE 0.018 0.001 PHE C 645 TRP 0.025 0.001 TRP C 789 HIS 0.005 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00410 (18516) covalent geometry : angle 0.65088 (25020) SS BOND : bond 0.00445 ( 10) SS BOND : angle 1.22521 ( 20) hydrogen bonds : bond 0.03753 ( 1067) hydrogen bonds : angle 4.22497 ( 3063) Misc. bond : bond 0.00497 ( 6) ********************** 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 356 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 353 time to evaluate : 0.527 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: A 429 MET cc_start: 0.7506 (mpp) cc_final: 0.7203 (mpp) REVERT: A 607 MET cc_start: 0.9069 (mmm) cc_final: 0.8480 (mmm) REVERT: A 730 MET cc_start: 0.8769 (mpp) cc_final: 0.8408 (mpp) REVERT: A 827 LEU cc_start: 0.9502 (tp) cc_final: 0.9251 (tp) REVERT: B 428 VAL cc_start: 0.9149 (t) cc_final: 0.8810 (t) REVERT: B 429 MET cc_start: 0.7472 (pmm) cc_final: 0.7077 (pmm) REVERT: B 447 CYS cc_start: 0.9131 (m) cc_final: 0.8334 (t) REVERT: B 485 MET cc_start: 0.8001 (mmm) cc_final: 0.7662 (mmt) REVERT: B 539 PHE cc_start: 0.9081 (p90) cc_final: 0.8819 (p90) REVERT: B 598 SER cc_start: 0.9308 (t) cc_final: 0.9030 (t) REVERT: B 607 MET cc_start: 0.9157 (mmt) cc_final: 0.8560 (mmm) REVERT: B 692 MET cc_start: 0.8727 (tmm) cc_final: 0.8155 (tmm) REVERT: B 696 MET cc_start: 0.7416 (mmm) cc_final: 0.6904 (mmm) REVERT: B 786 ASN cc_start: 0.9372 (t0) cc_final: 0.9120 (t0) REVERT: B 810 SER cc_start: 0.8721 (p) cc_final: 0.8478 (p) REVERT: C 485 MET cc_start: 0.7338 (mtp) cc_final: 0.6869 (mtp) REVERT: C 607 MET cc_start: 0.9228 (mmm) cc_final: 0.8337 (mmm) REVERT: C 819 TYR cc_start: 0.9224 (m-10) cc_final: 0.8909 (m-80) REVERT: D 525 MET cc_start: 0.9063 (tmm) cc_final: 0.8679 (tmm) REVERT: D 774 LYS cc_start: 0.9211 (ptpt) cc_final: 0.8616 (ptpp) REVERT: D 786 ASN cc_start: 0.8882 (m-40) cc_final: 0.8584 (m-40) REVERT: H 192 MET cc_start: 0.7854 (mmt) cc_final: 0.7644 (mmt) REVERT: F 10 MET cc_start: 0.8234 (tmm) cc_final: 0.7851 (tmm) REVERT: F 18 PHE cc_start: 0.8765 (t80) cc_final: 0.8562 (t80) REVERT: F 24 MET cc_start: 0.8839 (tpp) cc_final: 0.8487 (tpt) REVERT: F 174 TYR cc_start: 0.8271 (p90) cc_final: 0.7796 (p90) REVERT: G 117 MET cc_start: 0.8977 (mtp) cc_final: 0.8636 (mtt) REVERT: G 160 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8092 (t0) REVERT: G 195 VAL cc_start: 0.9285 (t) cc_final: 0.8990 (p) REVERT: E 113 ILE cc_start: 0.9593 (mt) cc_final: 0.9201 (mt) REVERT: E 117 MET cc_start: 0.8811 (mpp) cc_final: 0.8378 (mpp) REVERT: E 137 SER cc_start: 0.9211 (t) cc_final: 0.9009 (p) REVERT: E 191 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8571 (mm-30) outliers start: 3 outliers final: 1 residues processed: 354 average time/residue: 0.1201 time to fit residues: 65.9395 Evaluate side-chains 274 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 211 optimal weight: 0.0970 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN C 736 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.113568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084147 restraints weight = 53336.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084511 restraints weight = 40442.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084791 restraints weight = 40807.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085322 restraints weight = 28526.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085600 restraints weight = 26012.304| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.9867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18532 Z= 0.122 Angle : 0.605 8.511 25040 Z= 0.307 Chirality : 0.041 0.187 2800 Planarity : 0.004 0.046 3056 Dihedral : 7.438 116.034 2596 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.03 (0.18), residues: 2256 helix: 2.01 (0.15), residues: 1287 sheet: -1.35 (0.42), residues: 148 loop : -1.11 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 697 TYR 0.023 0.001 TYR A 695 PHE 0.021 0.001 PHE F 141 TRP 0.018 0.001 TRP C 789 HIS 0.005 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00272 (18516) covalent geometry : angle 0.60440 (25020) SS BOND : bond 0.00420 ( 10) SS BOND : angle 1.21055 ( 20) hydrogen bonds : bond 0.03498 ( 1067) hydrogen bonds : angle 4.09917 ( 3063) Misc. bond : bond 0.00464 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2981.23 seconds wall clock time: 53 minutes 11.74 seconds (3191.74 seconds total)