Starting phenix.real_space_refine on Thu Feb 5 15:48:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9f_71409/02_2026/9p9f_71409.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9f_71409/02_2026/9p9f_71409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9f_71409/02_2026/9p9f_71409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9f_71409/02_2026/9p9f_71409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9f_71409/02_2026/9p9f_71409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9f_71409/02_2026/9p9f_71409.map" } resolution = 3.89 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= 0.010 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 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18100 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Chain: "B" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Chain: "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: 4.17, per 1000 atoms: 0.23 Number of scatterers: 18100 At special positions: 0 Unit cell: (128.34, 109.74, 135.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 132 16.00 O 3252 8.00 N 2916 7.00 C 11796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 795 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 839.6 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: 102 helices and 23 sheets defined 59.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 445 through 459 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: 4.411A pdb=" N TRP A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 607 Processing helix chain 'A' and resid 617 through 648 removed outlier: 3.595A pdb=" N ALA A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 840 removed outlier: 3.561A 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 492 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 removed outlier: 5.259A pdb=" N PHE B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 607 Processing helix chain 'B' and resid 617 through 640 Processing helix chain 'B' and resid 641 through 646 removed outlier: 3.549A pdb=" N PHE B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 675 through 682 Processing helix chain 'B' and resid 686 through 699 Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 790 through 793 removed outlier: 3.656A pdb=" N GLY B 793 " --> pdb=" O TYR B 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 810 through 813 Processing helix chain 'B' and resid 814 through 840 removed outlier: 3.895A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 830 " --> pdb=" O GLY B 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 438 through 441 Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.617A pdb=" N SER C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 506 through 509 Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 544 through 566 removed outlier: 3.695A pdb=" N PHE C 563 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 607 removed outlier: 3.714A pdb=" N SER C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 642 removed outlier: 3.940A pdb=" N VAL C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 686 through 697 Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 764 through 778 removed outlier: 3.836A pdb=" N LEU C 773 " --> pdb=" O ASN C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 790 Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 838 removed outlier: 3.586A pdb=" N PHE C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 437 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 445 through 459 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 removed outlier: 3.943A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 607 Processing helix chain 'D' and resid 617 through 640 Processing helix chain 'D' and resid 641 through 646 removed outlier: 3.520A pdb=" N PHE D 645 " --> pdb=" O ASN D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 662 removed outlier: 3.849A pdb=" N LEU D 661 " --> pdb=" O SER D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 683 Processing helix chain 'D' and resid 686 through 698 removed outlier: 3.512A pdb=" N MET D 692 " --> pdb=" O VAL D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 717 Processing helix chain 'D' and resid 728 through 736 Processing helix chain 'D' and resid 764 through 778 Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 796 through 800 Processing helix chain 'D' and resid 810 through 813 Processing helix chain 'D' and resid 814 through 839 removed outlier: 3.716A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 30 removed outlier: 3.855A pdb=" N LEU H 12 " --> pdb=" O VAL H 8 " (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 207 removed outlier: 3.522A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'F' and resid 8 through 29 removed outlier: 3.866A pdb=" N THR F 14 " --> pdb=" O MET F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 125 removed outlier: 3.964A pdb=" N LEU F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 159 removed outlier: 3.713A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 207 removed outlier: 3.654A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.786A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (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 removed outlier: 3.720A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 207 removed outlier: 3.616A pdb=" N GLY G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'E' and resid 8 through 29 removed outlier: 3.689A pdb=" N LEU E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 removed outlier: 3.584A pdb=" N ARG E 99 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 132 through 160 Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.701A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 466 removed outlier: 3.706A pdb=" N THR A 421 " --> pdb=" O ALA A 465 " (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 513 Processing sheet with id=AA4, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.589A pdb=" N MET A 518 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 752 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 668 through 670 removed outlier: 5.988A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 462 through 466 Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=AA9, first strand: chain 'B' and resid 518 through 520 removed outlier: 4.195A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 668 through 670 removed outlier: 6.306A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU B 725 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY B 670 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N GLU B 727 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N PHE B 722 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS B 527 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 462 through 466 removed outlier: 6.508A pdb=" N VAL C 417 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA C 465 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL C 419 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C 496 " --> pdb=" O VAL C 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB4, first strand: chain 'C' and resid 511 through 520 removed outlier: 4.478A pdb=" N VAL C 756 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR C 754 " --> pdb=" O PRO C 516 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET C 518 " --> pdb=" O LYS C 752 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS C 752 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 668 through 670 removed outlier: 6.235A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 462 through 466 Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AB8, first strand: chain 'D' and resid 511 through 513 Processing sheet with id=AB9, first strand: chain 'D' and resid 518 through 520 removed outlier: 4.056A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 704 through 705 removed outlier: 8.266A pdb=" N THR D 705 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR D 671 " --> pdb=" O THR D 705 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU D 725 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N LEU D 672 " --> pdb=" O GLU D 727 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N PHE D 722 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS D 527 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AC3, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC4, first strand: chain 'G' and resid 76 through 79 removed outlier: 3.975A pdb=" N LEU G 76 " --> pdb=" O CYS G 68 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET G 58 " --> pdb=" O LEU G 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 78 through 79 1060 hydrogen bonds defined for protein. 3033 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: 3.57 Time building geometry restraints manager: 2.22 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 - 1.35: 5519 1.35 - 1.52: 7159 1.52 - 1.68: 5602 1.68 - 1.84: 220 Bond restraints: 18516 Sorted by residual: bond pdb=" C4 CYZ A 903 " pdb=" C5 CYZ A 903 " ideal model delta sigma weight residual 1.512 1.027 0.485 2.00e-02 2.50e+03 5.87e+02 bond pdb=" C4 CYZ B 903 " pdb=" C5 CYZ B 903 " 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 902 " pdb=" C5 CYZ B 902 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.79e+02 bond pdb=" C4 CYZ A 902 " pdb=" C5 CYZ A 902 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.79e+02 bond pdb=" C5 CYZ B 903 " pdb=" C6 CYZ B 903 " ideal model delta sigma weight residual 1.553 1.074 0.479 2.00e-02 2.50e+03 5.74e+02 ... (remaining 18511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 24913 4.59 - 9.19: 81 9.19 - 13.78: 7 13.78 - 18.37: 13 18.37 - 22.96: 6 Bond angle restraints: 25020 Sorted by residual: angle pdb=" C1 CYZ A 903 " pdb=" C2 CYZ A 903 " pdb=" C3 CYZ A 903 " ideal model delta sigma weight residual 106.92 129.88 -22.96 3.00e+00 1.11e-01 5.86e+01 angle pdb=" C9 CYZ A 903 " pdb=" S1 CYZ A 903 " pdb=" N1 CYZ A 903 " ideal model delta sigma weight residual 101.75 123.04 -21.29 3.00e+00 1.11e-01 5.04e+01 angle pdb=" C1 CYZ B 903 " pdb=" C2 CYZ B 903 " pdb=" C3 CYZ B 903 " ideal model delta sigma weight residual 106.92 128.04 -21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" C1 CYZ A 902 " pdb=" C2 CYZ A 902 " pdb=" C3 CYZ A 902 " ideal model delta sigma weight residual 106.92 128.01 -21.09 3.00e+00 1.11e-01 4.94e+01 angle pdb=" C1 CYZ B 902 " pdb=" C2 CYZ B 902 " pdb=" C3 CYZ B 902 " ideal model delta sigma weight residual 106.92 127.86 -20.94 3.00e+00 1.11e-01 4.87e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 10470 24.05 - 48.10: 370 48.10 - 72.15: 41 72.15 - 96.21: 25 96.21 - 120.26: 7 Dihedral angle restraints: 10913 sinusoidal: 4317 harmonic: 6596 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 151.64 -58.64 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA GLU D 794 " pdb=" C GLU D 794 " pdb=" N CYS D 795 " pdb=" CA CYS D 795 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA PRO D 701 " pdb=" C PRO D 701 " pdb=" N SER D 702 " pdb=" CA SER D 702 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.427: 2786 0.427 - 0.853: 6 0.853 - 1.280: 0 1.280 - 1.707: 0 1.707 - 2.134: 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 2.13 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" C5 CYZ A 902 " pdb=" C4 CYZ A 902 " pdb=" C6 CYZ A 902 " pdb=" C7 CYZ A 902 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.13 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 2.13 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=" CD ARG D 507 " -0.255 9.50e-02 1.11e+02 1.15e-01 1.08e+01 pdb=" NE ARG D 507 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 507 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG D 507 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D 507 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 CYZ B 902 " 0.009 2.00e-02 2.50e+03 1.80e-02 8.13e+00 pdb=" C11 CYZ B 902 " 0.040 2.00e-02 2.50e+03 pdb=" C12 CYZ B 902 " -0.010 2.00e-02 2.50e+03 pdb=" C13 CYZ B 902 " -0.004 2.00e-02 2.50e+03 pdb=" C14 CYZ B 902 " 0.002 2.00e-02 2.50e+03 pdb=" C9 CYZ B 902 " 0.018 2.00e-02 2.50e+03 pdb=" N2 CYZ B 902 " -0.012 2.00e-02 2.50e+03 pdb=" S1 CYZ B 902 " -0.025 2.00e-02 2.50e+03 pdb=" S2 CYZ B 902 " -0.018 2.00e-02 2.50e+03 pdb="CL CYZ B 902 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 546 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C GLU C 546 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU C 546 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 547 " -0.016 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 2 2.00 - 2.73: 967 2.73 - 3.45: 28210 3.45 - 4.18: 42417 4.18 - 4.90: 77081 Nonbonded interactions: 148677 Sorted by model distance: nonbonded pdb=" OG SER A 751 " pdb=" C10 CYZ A 903 " model vdw 1.276 2.608 nonbonded pdb=" OG SER A 751 " pdb=" N2 CYZ A 903 " model vdw 1.542 3.120 nonbonded pdb=" OG SER D 519 " pdb=" O1 CYZ A 903 " model vdw 2.060 3.040 nonbonded pdb=" CA SER A 751 " pdb=" C10 CYZ A 903 " model vdw 2.075 2.952 nonbonded pdb=" OG SER A 519 " pdb=" O2 CYZ A 902 " model vdw 2.143 3.040 ... (remaining 148672 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.485 18530 Z= 0.829 Angle : 0.917 22.963 25042 Z= 0.444 Chirality : 0.123 2.134 2800 Planarity : 0.007 0.115 3056 Dihedral : 13.833 120.258 6672 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.19 % Favored : 94.41 % Rotamer: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % 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: -1.12 (0.16), residues: 2256 helix: -0.36 (0.13), residues: 1253 sheet: -0.75 (0.43), residues: 139 loop : -1.14 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG D 507 TYR 0.025 0.004 TYR B 669 PHE 0.033 0.002 PHE D 517 TRP 0.032 0.002 TRP C 788 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.01636 (18516) covalent geometry : angle 0.91683 (25020) SS BOND : bond 0.00275 ( 11) SS BOND : angle 0.57359 ( 22) hydrogen bonds : bond 0.12438 ( 1060) hydrogen bonds : angle 6.33105 ( 3033) Misc. bond : bond 0.12419 ( 3) *********************** 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 373 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.645 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 485 MET cc_start: 0.8306 (mtm) cc_final: 0.8009 (mtt) REVERT: A 607 MET cc_start: 0.8605 (mmm) cc_final: 0.8245 (mmm) REVERT: A 743 MET cc_start: 0.8346 (ptm) cc_final: 0.7722 (ppp) REVERT: A 748 ASN cc_start: 0.8880 (m-40) cc_final: 0.8490 (m110) REVERT: B 607 MET cc_start: 0.8864 (mmt) cc_final: 0.8499 (mmm) REVERT: B 608 GLN cc_start: 0.8319 (mt0) cc_final: 0.7894 (tm-30) REVERT: B 630 PHE cc_start: 0.8755 (t80) cc_final: 0.8508 (t80) REVERT: B 692 MET cc_start: 0.9396 (mmt) cc_final: 0.8902 (mmm) REVERT: C 433 ASN cc_start: 0.9275 (t0) cc_final: 0.9072 (p0) REVERT: C 446 TYR cc_start: 0.9025 (t80) cc_final: 0.8801 (t80) REVERT: C 485 MET cc_start: 0.8152 (mtm) cc_final: 0.7239 (mtt) REVERT: C 525 MET cc_start: 0.8215 (tmm) cc_final: 0.8010 (tmm) REVERT: C 541 ASP cc_start: 0.8906 (m-30) cc_final: 0.8582 (m-30) REVERT: C 607 MET cc_start: 0.8943 (mmm) cc_final: 0.8444 (mmm) REVERT: C 730 MET cc_start: 0.9418 (mtm) cc_final: 0.9079 (mtp) REVERT: D 485 MET cc_start: 0.8748 (mtm) cc_final: 0.8312 (mtt) REVERT: D 749 LEU cc_start: 0.9430 (mt) cc_final: 0.8928 (tt) REVERT: D 785 LYS cc_start: 0.9031 (tttt) cc_final: 0.8435 (tppt) REVERT: D 790 TYR cc_start: 0.8380 (m-80) cc_final: 0.8024 (m-80) REVERT: H 117 MET cc_start: 0.8771 (mmm) cc_final: 0.8531 (mmm) REVERT: F 10 MET cc_start: 0.8476 (ttt) cc_final: 0.7984 (tmm) REVERT: F 31 ASP cc_start: 0.8189 (m-30) cc_final: 0.7714 (m-30) REVERT: F 154 ILE cc_start: 0.9428 (mt) cc_final: 0.9202 (tp) REVERT: F 160 ASN cc_start: 0.8131 (t0) cc_final: 0.7894 (t0) REVERT: G 10 MET cc_start: 0.8824 (mpp) cc_final: 0.8405 (mpp) REVERT: G 110 LEU cc_start: 0.9624 (tp) cc_final: 0.9414 (tp) REVERT: G 117 MET cc_start: 0.9259 (mtm) cc_final: 0.9054 (tpt) REVERT: G 181 TYR cc_start: 0.8915 (m-80) cc_final: 0.8680 (m-10) REVERT: E 30 THR cc_start: 0.8756 (p) cc_final: 0.8536 (p) REVERT: E 37 ARG cc_start: 0.9072 (mmt90) cc_final: 0.8758 (mmp80) REVERT: E 117 MET cc_start: 0.8890 (tpp) cc_final: 0.8240 (tpt) REVERT: E 121 CYS cc_start: 0.8769 (m) cc_final: 0.8237 (m) REVERT: E 156 TYR cc_start: 0.9165 (t80) cc_final: 0.8914 (t80) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.1301 time to fit residues: 74.2564 Evaluate side-chains 248 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 0.5980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047935 restraints weight = 93793.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.049388 restraints weight = 52286.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050374 restraints weight = 35789.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051080 restraints weight = 27801.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051531 restraints weight = 23301.424| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18530 Z= 0.178 Angle : 0.683 10.867 25042 Z= 0.353 Chirality : 0.045 0.314 2800 Planarity : 0.004 0.040 3056 Dihedral : 9.972 125.590 2596 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 1.40 % Allowed : 9.30 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2256 helix: 1.58 (0.15), residues: 1263 sheet: -0.69 (0.36), residues: 199 loop : -0.73 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 507 TYR 0.031 0.002 TYR A 819 PHE 0.024 0.002 PHE B 517 TRP 0.017 0.002 TRP G 178 HIS 0.005 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00384 (18516) covalent geometry : angle 0.68338 (25020) SS BOND : bond 0.00250 ( 11) SS BOND : angle 0.63019 ( 22) hydrogen bonds : bond 0.04094 ( 1060) hydrogen bonds : angle 4.72355 ( 3033) Misc. bond : bond 0.00701 ( 3) *********************** 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 315 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 MET cc_start: 0.9442 (mpp) cc_final: 0.9034 (ppp) REVERT: A 485 MET cc_start: 0.8772 (mtm) cc_final: 0.8454 (mtt) REVERT: A 525 MET cc_start: 0.8384 (tmm) cc_final: 0.8106 (tpp) REVERT: A 607 MET cc_start: 0.9328 (mmm) cc_final: 0.9095 (mmm) REVERT: A 743 MET cc_start: 0.8227 (ptm) cc_final: 0.7331 (ppp) REVERT: A 819 TYR cc_start: 0.8998 (m-80) cc_final: 0.8575 (m-80) REVERT: B 485 MET cc_start: 0.9528 (mtm) cc_final: 0.9162 (mtm) REVERT: B 525 MET cc_start: 0.9182 (ttp) cc_final: 0.8805 (tmm) REVERT: B 607 MET cc_start: 0.9340 (mmt) cc_final: 0.8686 (mmt) REVERT: B 608 GLN cc_start: 0.9322 (mt0) cc_final: 0.8333 (tm-30) REVERT: B 641 ASN cc_start: 0.8416 (t0) cc_final: 0.8063 (t0) REVERT: B 692 MET cc_start: 0.9549 (mmt) cc_final: 0.9187 (mmm) REVERT: C 436 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8518 (ppp) REVERT: C 472 TYR cc_start: 0.9144 (m-80) cc_final: 0.8796 (m-80) REVERT: C 518 MET cc_start: 0.9257 (mtp) cc_final: 0.8856 (mtm) REVERT: C 541 ASP cc_start: 0.9262 (m-30) cc_final: 0.8941 (m-30) REVERT: C 563 PHE cc_start: 0.3076 (OUTLIER) cc_final: 0.1879 (m-10) REVERT: C 819 TYR cc_start: 0.8831 (m-80) cc_final: 0.8598 (m-80) REVERT: D 485 MET cc_start: 0.9159 (mtm) cc_final: 0.8612 (mtt) REVERT: D 743 MET cc_start: 0.8776 (tpp) cc_final: 0.8470 (tpp) REVERT: D 749 LEU cc_start: 0.9673 (mt) cc_final: 0.9200 (tt) REVERT: D 785 LYS cc_start: 0.9647 (tttt) cc_final: 0.8860 (tppt) REVERT: D 790 TYR cc_start: 0.8865 (m-80) cc_final: 0.8196 (m-80) REVERT: H 117 MET cc_start: 0.9310 (mmm) cc_final: 0.9024 (mmm) REVERT: H 185 LEU cc_start: 0.9291 (tp) cc_final: 0.9086 (tp) REVERT: F 10 MET cc_start: 0.8801 (ttt) cc_final: 0.8070 (tmm) REVERT: F 31 ASP cc_start: 0.8688 (m-30) cc_final: 0.8217 (m-30) REVERT: F 154 ILE cc_start: 0.9614 (mt) cc_final: 0.9323 (tp) REVERT: F 160 ASN cc_start: 0.8879 (t0) cc_final: 0.8673 (t0) REVERT: F 200 MET cc_start: 0.9666 (ttp) cc_final: 0.9441 (mtm) REVERT: G 10 MET cc_start: 0.8945 (mpp) cc_final: 0.8664 (mpp) REVERT: G 63 LEU cc_start: 0.9302 (mt) cc_final: 0.8860 (pt) REVERT: G 117 MET cc_start: 0.9335 (mtm) cc_final: 0.9004 (tpt) REVERT: E 37 ARG cc_start: 0.9026 (mmt90) cc_final: 0.8528 (mmp80) REVERT: E 117 MET cc_start: 0.9257 (tpp) cc_final: 0.8509 (tpt) REVERT: E 121 CYS cc_start: 0.8939 (m) cc_final: 0.8335 (m) REVERT: E 151 ILE cc_start: 0.9837 (mm) cc_final: 0.9562 (tp) outliers start: 27 outliers final: 16 residues processed: 301 average time/residue: 0.1237 time to fit residues: 58.3821 Evaluate side-chains 255 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN B 609 GLN B 731 ASN ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.062398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.045875 restraints weight = 98279.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047229 restraints weight = 55318.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048199 restraints weight = 38391.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.048882 restraints weight = 29881.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049260 restraints weight = 25146.800| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 18530 Z= 0.264 Angle : 0.696 9.996 25042 Z= 0.365 Chirality : 0.044 0.245 2800 Planarity : 0.004 0.048 3056 Dihedral : 9.523 115.382 2596 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.55 % Allowed : 11.95 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % 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: 0.93 (0.19), residues: 2256 helix: 1.69 (0.15), residues: 1279 sheet: -1.06 (0.34), residues: 203 loop : -0.67 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 650 TYR 0.029 0.002 TYR A 819 PHE 0.028 0.002 PHE C 563 TRP 0.012 0.002 TRP D 788 HIS 0.005 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00560 (18516) covalent geometry : angle 0.69639 (25020) SS BOND : bond 0.00230 ( 11) SS BOND : angle 0.33384 ( 22) hydrogen bonds : bond 0.04068 ( 1060) hydrogen bonds : angle 4.77241 ( 3033) Misc. bond : bond 0.01080 ( 3) *********************** 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 276 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 MET cc_start: 0.9464 (mpp) cc_final: 0.8995 (ppp) REVERT: A 485 MET cc_start: 0.8743 (mtm) cc_final: 0.8420 (mtt) REVERT: A 508 GLU cc_start: 0.8747 (tt0) cc_final: 0.8328 (tm-30) REVERT: A 743 MET cc_start: 0.8238 (ptm) cc_final: 0.7424 (ppp) REVERT: A 770 LEU cc_start: 0.9423 (mm) cc_final: 0.9157 (pp) REVERT: A 819 TYR cc_start: 0.9020 (m-80) cc_final: 0.8500 (m-80) REVERT: B 463 LYS cc_start: 0.9674 (ptpt) cc_final: 0.9414 (tptt) REVERT: B 485 MET cc_start: 0.9553 (mtm) cc_final: 0.9268 (mtm) REVERT: B 607 MET cc_start: 0.9411 (mmt) cc_final: 0.8895 (mmt) REVERT: B 641 ASN cc_start: 0.8593 (t0) cc_final: 0.8325 (t0) REVERT: B 819 TYR cc_start: 0.9318 (m-80) cc_final: 0.9075 (m-80) REVERT: C 446 TYR cc_start: 0.9754 (t80) cc_final: 0.9395 (t80) REVERT: C 485 MET cc_start: 0.8818 (mtm) cc_final: 0.8350 (mpp) REVERT: C 518 MET cc_start: 0.9390 (mtp) cc_final: 0.8712 (mtp) REVERT: C 520 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8293 (pt) REVERT: C 541 ASP cc_start: 0.9284 (m-30) cc_final: 0.8975 (m-30) REVERT: C 563 PHE cc_start: 0.3358 (OUTLIER) cc_final: 0.2440 (m-10) REVERT: C 607 MET cc_start: 0.9710 (tpp) cc_final: 0.9499 (tpp) REVERT: D 485 MET cc_start: 0.9179 (mtm) cc_final: 0.8617 (mtt) REVERT: D 692 MET cc_start: 0.9046 (mmm) cc_final: 0.8789 (mmm) REVERT: D 785 LYS cc_start: 0.9655 (tttt) cc_final: 0.8833 (tppt) REVERT: D 790 TYR cc_start: 0.8875 (m-80) cc_final: 0.8122 (m-80) REVERT: H 24 MET cc_start: 0.9423 (tpt) cc_final: 0.9159 (tpt) REVERT: H 117 MET cc_start: 0.9330 (mmm) cc_final: 0.9019 (mmm) REVERT: F 10 MET cc_start: 0.8880 (ttt) cc_final: 0.8066 (tmm) REVERT: F 31 ASP cc_start: 0.8735 (m-30) cc_final: 0.8364 (m-30) REVERT: F 160 ASN cc_start: 0.8941 (t0) cc_final: 0.8733 (t0) REVERT: F 200 MET cc_start: 0.9675 (ttp) cc_final: 0.9439 (mtm) REVERT: F 206 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8904 (tptt) REVERT: G 10 MET cc_start: 0.9207 (mpp) cc_final: 0.8941 (mpp) REVERT: G 63 LEU cc_start: 0.9316 (mt) cc_final: 0.8917 (pt) REVERT: G 70 GLU cc_start: 0.8674 (tt0) cc_final: 0.8423 (tm-30) REVERT: G 117 MET cc_start: 0.9324 (mtm) cc_final: 0.9019 (tpt) REVERT: E 37 ARG cc_start: 0.9108 (mmt90) cc_final: 0.8556 (mmp80) REVERT: E 117 MET cc_start: 0.9280 (tpp) cc_final: 0.8516 (tpt) REVERT: E 121 CYS cc_start: 0.8985 (m) cc_final: 0.8439 (m) outliers start: 49 outliers final: 29 residues processed: 259 average time/residue: 0.1213 time to fit residues: 50.0295 Evaluate side-chains 242 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 114 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 211 optimal weight: 0.0470 chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 ASN C 609 GLN D 641 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047063 restraints weight = 94954.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048464 restraints weight = 53432.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.049468 restraints weight = 36678.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050123 restraints weight = 28435.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050495 restraints weight = 23930.821| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 18530 Z= 0.162 Angle : 0.629 11.295 25042 Z= 0.320 Chirality : 0.043 0.258 2800 Planarity : 0.004 0.052 3056 Dihedral : 9.184 116.546 2596 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.18 % Allowed : 12.89 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2256 helix: 2.04 (0.15), residues: 1272 sheet: -1.31 (0.34), residues: 203 loop : -0.67 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 737 TYR 0.021 0.001 TYR A 819 PHE 0.019 0.001 PHE B 517 TRP 0.012 0.001 TRP D 788 HIS 0.018 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00354 (18516) covalent geometry : angle 0.62911 (25020) SS BOND : bond 0.00146 ( 11) SS BOND : angle 0.35023 ( 22) hydrogen bonds : bond 0.03616 ( 1060) hydrogen bonds : angle 4.40554 ( 3033) Misc. bond : bond 0.01043 ( 3) *********************** 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 285 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.679 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 436 MET cc_start: 0.9428 (mpp) cc_final: 0.8872 (ppp) REVERT: A 485 MET cc_start: 0.8789 (mtm) cc_final: 0.8451 (mtt) REVERT: A 508 GLU cc_start: 0.8700 (tt0) cc_final: 0.8432 (tm-30) REVERT: A 743 MET cc_start: 0.8579 (ptm) cc_final: 0.8313 (ptm) REVERT: A 770 LEU cc_start: 0.9392 (mm) cc_final: 0.9119 (pp) REVERT: A 819 TYR cc_start: 0.9026 (m-80) cc_final: 0.8542 (m-80) REVERT: B 463 LYS cc_start: 0.9669 (ptpt) cc_final: 0.9414 (tptt) REVERT: B 525 MET cc_start: 0.8426 (tmm) cc_final: 0.7945 (tmm) REVERT: B 607 MET cc_start: 0.9335 (mmt) cc_final: 0.8874 (mmm) REVERT: B 641 ASN cc_start: 0.8547 (t0) cc_final: 0.8204 (t0) REVERT: B 651 MET cc_start: 0.9164 (ppp) cc_final: 0.8642 (tmm) REVERT: B 743 MET cc_start: 0.9061 (ppp) cc_final: 0.8395 (ppp) REVERT: C 446 TYR cc_start: 0.9750 (t80) cc_final: 0.9115 (t80) REVERT: C 472 TYR cc_start: 0.9103 (m-80) cc_final: 0.8753 (m-80) REVERT: C 518 MET cc_start: 0.9340 (mtp) cc_final: 0.8549 (mtt) REVERT: C 520 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8285 (pt) REVERT: C 541 ASP cc_start: 0.9254 (m-30) cc_final: 0.8998 (m-30) REVERT: C 563 PHE cc_start: 0.3282 (OUTLIER) cc_final: 0.2318 (m-10) REVERT: C 607 MET cc_start: 0.9696 (tpp) cc_final: 0.9304 (tpp) REVERT: D 436 MET cc_start: 0.9536 (OUTLIER) cc_final: 0.9332 (tmm) REVERT: D 485 MET cc_start: 0.9133 (mtm) cc_final: 0.8565 (mtt) REVERT: D 696 MET cc_start: 0.9272 (mmt) cc_final: 0.8992 (mmp) REVERT: D 773 LEU cc_start: 0.9819 (OUTLIER) cc_final: 0.9535 (tp) REVERT: D 785 LYS cc_start: 0.9628 (tttt) cc_final: 0.8902 (tppt) REVERT: D 790 TYR cc_start: 0.8853 (m-80) cc_final: 0.8110 (m-80) REVERT: H 24 MET cc_start: 0.9389 (tpt) cc_final: 0.9135 (tpt) REVERT: H 117 MET cc_start: 0.9337 (mmm) cc_final: 0.9015 (mmm) REVERT: H 191 GLU cc_start: 0.9425 (mm-30) cc_final: 0.9096 (mm-30) REVERT: F 10 MET cc_start: 0.8853 (ttt) cc_final: 0.8026 (tmm) REVERT: F 31 ASP cc_start: 0.8697 (m-30) cc_final: 0.8336 (m-30) REVERT: F 160 ASN cc_start: 0.8917 (t0) cc_final: 0.8701 (t0) REVERT: F 200 MET cc_start: 0.9669 (ttp) cc_final: 0.9412 (mtm) REVERT: F 206 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8916 (tptt) REVERT: G 63 LEU cc_start: 0.9249 (mt) cc_final: 0.8944 (pt) REVERT: G 117 MET cc_start: 0.9302 (mtm) cc_final: 0.8979 (tpt) REVERT: E 37 ARG cc_start: 0.9100 (mmt90) cc_final: 0.8673 (mmp80) REVERT: E 117 MET cc_start: 0.9245 (tpp) cc_final: 0.8397 (tpt) REVERT: E 121 CYS cc_start: 0.8996 (m) cc_final: 0.8407 (m) REVERT: E 151 ILE cc_start: 0.9856 (mm) cc_final: 0.9617 (tp) outliers start: 42 outliers final: 21 residues processed: 268 average time/residue: 0.1152 time to fit residues: 49.3167 Evaluate side-chains 240 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN C 609 GLN D 641 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047115 restraints weight = 95233.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.048460 restraints weight = 53610.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049451 restraints weight = 37186.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050121 restraints weight = 28673.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.050574 restraints weight = 24028.661| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18530 Z= 0.170 Angle : 0.643 11.134 25042 Z= 0.325 Chirality : 0.043 0.262 2800 Planarity : 0.004 0.054 3056 Dihedral : 8.883 115.882 2596 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.49 % Allowed : 14.19 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % 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: 1.26 (0.19), residues: 2256 helix: 2.12 (0.15), residues: 1263 sheet: -1.50 (0.33), residues: 221 loop : -0.58 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.022 0.001 TYR C 555 PHE 0.020 0.001 PHE C 563 TRP 0.011 0.001 TRP D 788 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00371 (18516) covalent geometry : angle 0.64277 (25020) SS BOND : bond 0.00153 ( 11) SS BOND : angle 0.31926 ( 22) hydrogen bonds : bond 0.03591 ( 1060) hydrogen bonds : angle 4.40463 ( 3033) Misc. bond : bond 0.00971 ( 3) *********************** 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 284 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.667 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: A 436 MET cc_start: 0.9437 (mpp) cc_final: 0.8849 (ppp) REVERT: A 485 MET cc_start: 0.8806 (mtm) cc_final: 0.8472 (mtt) REVERT: A 508 GLU cc_start: 0.8781 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 743 MET cc_start: 0.8659 (ptm) cc_final: 0.8443 (ptm) REVERT: A 819 TYR cc_start: 0.9002 (m-80) cc_final: 0.8433 (m-80) REVERT: A 820 ILE cc_start: 0.9280 (tt) cc_final: 0.8970 (tp) REVERT: B 463 LYS cc_start: 0.9659 (ptpt) cc_final: 0.9418 (tptt) REVERT: B 524 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9213 (tp) REVERT: B 607 MET cc_start: 0.9432 (mmt) cc_final: 0.8847 (mmm) REVERT: B 641 ASN cc_start: 0.8595 (t0) cc_final: 0.8220 (t0) REVERT: B 651 MET cc_start: 0.9083 (ppp) cc_final: 0.8602 (tmm) REVERT: B 743 MET cc_start: 0.9083 (ppp) cc_final: 0.8479 (ppp) REVERT: C 429 MET cc_start: 0.8729 (mpp) cc_final: 0.8512 (mpp) REVERT: C 446 TYR cc_start: 0.9734 (t80) cc_final: 0.9487 (t80) REVERT: C 472 TYR cc_start: 0.9073 (m-80) cc_final: 0.8740 (m-80) REVERT: C 518 MET cc_start: 0.9305 (mtp) cc_final: 0.8871 (mtm) REVERT: C 520 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8348 (pt) REVERT: C 541 ASP cc_start: 0.9264 (m-30) cc_final: 0.8939 (t0) REVERT: C 563 PHE cc_start: 0.3311 (OUTLIER) cc_final: 0.2323 (m-10) REVERT: C 607 MET cc_start: 0.9652 (tpp) cc_final: 0.9402 (tpp) REVERT: C 683 ARG cc_start: 0.9258 (mmt180) cc_final: 0.9055 (ttp80) REVERT: D 429 MET cc_start: 0.8490 (mpp) cc_final: 0.8021 (mpp) REVERT: D 436 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.9274 (tmm) REVERT: D 485 MET cc_start: 0.9100 (mtm) cc_final: 0.8542 (mtt) REVERT: D 696 MET cc_start: 0.9249 (mmt) cc_final: 0.8989 (mmp) REVERT: D 773 LEU cc_start: 0.9815 (OUTLIER) cc_final: 0.9530 (tp) REVERT: D 785 LYS cc_start: 0.9605 (tttt) cc_final: 0.9356 (tptt) REVERT: H 24 MET cc_start: 0.9405 (tpt) cc_final: 0.9130 (tpt) REVERT: H 117 MET cc_start: 0.9268 (mmm) cc_final: 0.8928 (mmm) REVERT: F 10 MET cc_start: 0.8849 (ttt) cc_final: 0.7990 (tmm) REVERT: F 31 ASP cc_start: 0.8771 (m-30) cc_final: 0.8366 (m-30) REVERT: F 160 ASN cc_start: 0.8972 (t0) cc_final: 0.8741 (t0) REVERT: F 200 MET cc_start: 0.9663 (ttp) cc_final: 0.9423 (mtm) REVERT: F 206 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8930 (tptt) REVERT: G 63 LEU cc_start: 0.9241 (mt) cc_final: 0.8959 (pt) REVERT: G 117 MET cc_start: 0.9276 (mtm) cc_final: 0.9007 (tpt) REVERT: G 206 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8557 (mmtp) REVERT: E 37 ARG cc_start: 0.9087 (mmt90) cc_final: 0.8618 (mmp80) REVERT: E 70 GLU cc_start: 0.8775 (pp20) cc_final: 0.8554 (pp20) REVERT: E 117 MET cc_start: 0.9265 (tpp) cc_final: 0.8384 (tpt) REVERT: E 121 CYS cc_start: 0.8991 (m) cc_final: 0.8387 (m) REVERT: E 151 ILE cc_start: 0.9859 (mm) cc_final: 0.9607 (tp) outliers start: 48 outliers final: 33 residues processed: 265 average time/residue: 0.1073 time to fit residues: 45.8937 Evaluate side-chains 251 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 109 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 204 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN D 641 ASN G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047035 restraints weight = 95757.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048385 restraints weight = 54427.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049360 restraints weight = 37760.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.050026 restraints weight = 29358.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050405 restraints weight = 24700.218| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18530 Z= 0.183 Angle : 0.668 13.430 25042 Z= 0.336 Chirality : 0.043 0.263 2800 Planarity : 0.004 0.056 3056 Dihedral : 8.511 114.507 2596 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 2.60 % Allowed : 15.38 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % 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: 1.19 (0.19), residues: 2256 helix: 2.06 (0.15), residues: 1261 sheet: -1.50 (0.34), residues: 221 loop : -0.60 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 737 TYR 0.026 0.001 TYR F 156 PHE 0.020 0.001 PHE C 563 TRP 0.010 0.001 TRP G 178 HIS 0.003 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00397 (18516) covalent geometry : angle 0.66800 (25020) SS BOND : bond 0.00223 ( 11) SS BOND : angle 0.49497 ( 22) hydrogen bonds : bond 0.03601 ( 1060) hydrogen bonds : angle 4.42473 ( 3033) Misc. bond : bond 0.00955 ( 3) *********************** 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 271 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.642 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: A 436 MET cc_start: 0.9453 (mpp) cc_final: 0.8877 (ppp) REVERT: A 485 MET cc_start: 0.8791 (mtm) cc_final: 0.8459 (mtt) REVERT: A 508 GLU cc_start: 0.8827 (tt0) cc_final: 0.8195 (tm-30) REVERT: A 509 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8478 (mm-30) REVERT: A 736 GLN cc_start: 0.9664 (mm-40) cc_final: 0.9144 (mt0) REVERT: A 743 MET cc_start: 0.8591 (ptm) cc_final: 0.8387 (ptm) REVERT: A 819 TYR cc_start: 0.8970 (m-80) cc_final: 0.8405 (m-80) REVERT: A 820 ILE cc_start: 0.9382 (tt) cc_final: 0.9077 (tp) REVERT: B 463 LYS cc_start: 0.9655 (ptpt) cc_final: 0.9413 (tptt) REVERT: B 485 MET cc_start: 0.9524 (mtm) cc_final: 0.8762 (mtm) REVERT: B 525 MET cc_start: 0.8388 (tmm) cc_final: 0.7971 (tpp) REVERT: B 607 MET cc_start: 0.9409 (mmt) cc_final: 0.8792 (mmm) REVERT: B 608 GLN cc_start: 0.9132 (mp10) cc_final: 0.8729 (mp10) REVERT: B 641 ASN cc_start: 0.8622 (t0) cc_final: 0.8257 (t0) REVERT: B 651 MET cc_start: 0.9053 (ppp) cc_final: 0.8683 (tmm) REVERT: B 696 MET cc_start: 0.9007 (tpt) cc_final: 0.8672 (tpp) REVERT: B 743 MET cc_start: 0.9077 (ppp) cc_final: 0.8643 (ppp) REVERT: C 472 TYR cc_start: 0.9073 (m-80) cc_final: 0.8469 (m-80) REVERT: C 485 MET cc_start: 0.8229 (mtm) cc_final: 0.7397 (mtm) REVERT: C 518 MET cc_start: 0.9297 (mtp) cc_final: 0.8858 (mtm) REVERT: C 520 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8382 (pt) REVERT: C 541 ASP cc_start: 0.9253 (m-30) cc_final: 0.8953 (t0) REVERT: C 563 PHE cc_start: 0.3343 (OUTLIER) cc_final: 0.2328 (m-10) REVERT: C 607 MET cc_start: 0.9674 (tpp) cc_final: 0.9454 (tpp) REVERT: C 692 MET cc_start: 0.9394 (mmm) cc_final: 0.9110 (mmm) REVERT: C 730 MET cc_start: 0.9725 (mtp) cc_final: 0.9248 (ptp) REVERT: D 429 MET cc_start: 0.8454 (mpp) cc_final: 0.8022 (mpp) REVERT: D 433 ASN cc_start: 0.9460 (p0) cc_final: 0.9030 (p0) REVERT: D 485 MET cc_start: 0.9103 (mtm) cc_final: 0.8497 (mtt) REVERT: D 696 MET cc_start: 0.9271 (mmt) cc_final: 0.8989 (mmp) REVERT: D 773 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9488 (tp) REVERT: D 785 LYS cc_start: 0.9588 (tttt) cc_final: 0.9330 (ptpp) REVERT: H 58 MET cc_start: 0.7554 (tpp) cc_final: 0.7320 (tpp) REVERT: H 189 ILE cc_start: 0.9566 (mm) cc_final: 0.9160 (tt) REVERT: H 191 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9021 (mm-30) REVERT: F 10 MET cc_start: 0.8845 (ttt) cc_final: 0.7991 (tmm) REVERT: F 31 ASP cc_start: 0.8755 (m-30) cc_final: 0.8376 (m-30) REVERT: F 160 ASN cc_start: 0.8987 (t0) cc_final: 0.8750 (t0) REVERT: F 200 MET cc_start: 0.9660 (ttp) cc_final: 0.9434 (mtm) REVERT: G 12 LEU cc_start: 0.9810 (OUTLIER) cc_final: 0.9493 (mm) REVERT: G 63 LEU cc_start: 0.9215 (mt) cc_final: 0.8952 (pt) REVERT: G 117 MET cc_start: 0.9294 (mtm) cc_final: 0.9010 (tpt) REVERT: G 206 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8632 (mmtt) REVERT: E 37 ARG cc_start: 0.9082 (mmt90) cc_final: 0.8628 (mmp80) REVERT: E 70 GLU cc_start: 0.8797 (pp20) cc_final: 0.8562 (pp20) REVERT: E 117 MET cc_start: 0.9251 (tpp) cc_final: 0.8371 (tpt) REVERT: E 121 CYS cc_start: 0.8955 (m) cc_final: 0.8288 (m) REVERT: E 151 ILE cc_start: 0.9850 (mm) cc_final: 0.9614 (tp) outliers start: 50 outliers final: 40 residues processed: 254 average time/residue: 0.1140 time to fit residues: 46.5272 Evaluate side-chains 257 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048168 restraints weight = 95198.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049556 restraints weight = 53166.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.050564 restraints weight = 36615.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051264 restraints weight = 28196.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051629 restraints weight = 23489.725| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18530 Z= 0.132 Angle : 0.652 12.212 25042 Z= 0.321 Chirality : 0.043 0.255 2800 Planarity : 0.004 0.056 3056 Dihedral : 8.177 113.122 2596 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 2.29 % Allowed : 16.58 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.19), residues: 2256 helix: 2.11 (0.15), residues: 1269 sheet: -1.39 (0.37), residues: 191 loop : -0.58 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 683 TYR 0.029 0.001 TYR D 669 PHE 0.016 0.001 PHE B 517 TRP 0.010 0.001 TRP G 178 HIS 0.003 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00290 (18516) covalent geometry : angle 0.65171 (25020) SS BOND : bond 0.00164 ( 11) SS BOND : angle 0.42854 ( 22) hydrogen bonds : bond 0.03424 ( 1060) hydrogen bonds : angle 4.19234 ( 3033) Misc. bond : bond 0.00947 ( 3) *********************** 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 275 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.8590 (mpp) cc_final: 0.8190 (mpp) REVERT: A 436 MET cc_start: 0.9447 (mpp) cc_final: 0.9019 (ppp) REVERT: A 485 MET cc_start: 0.8825 (mtm) cc_final: 0.8485 (mtt) REVERT: A 508 GLU cc_start: 0.8807 (tt0) cc_final: 0.8549 (tm-30) REVERT: A 736 GLN cc_start: 0.9646 (mm-40) cc_final: 0.9135 (mt0) REVERT: A 820 ILE cc_start: 0.9328 (tt) cc_final: 0.9017 (tp) REVERT: B 463 LYS cc_start: 0.9658 (ptpt) cc_final: 0.9429 (tptt) REVERT: B 485 MET cc_start: 0.9504 (mtm) cc_final: 0.8841 (mtm) REVERT: B 525 MET cc_start: 0.8386 (tmm) cc_final: 0.7810 (tpp) REVERT: B 607 MET cc_start: 0.9356 (mmt) cc_final: 0.8853 (mmm) REVERT: B 608 GLN cc_start: 0.9081 (mp10) cc_final: 0.8813 (mp10) REVERT: B 641 ASN cc_start: 0.8684 (t0) cc_final: 0.8320 (t0) REVERT: B 651 MET cc_start: 0.9014 (ppp) cc_final: 0.8706 (tmm) REVERT: B 696 MET cc_start: 0.8934 (tpt) cc_final: 0.8574 (tpp) REVERT: B 743 MET cc_start: 0.9091 (ppp) cc_final: 0.8667 (ppp) REVERT: C 472 TYR cc_start: 0.9058 (m-80) cc_final: 0.8441 (m-80) REVERT: C 485 MET cc_start: 0.8299 (mtm) cc_final: 0.7576 (mtm) REVERT: C 518 MET cc_start: 0.9279 (mtp) cc_final: 0.8893 (mtm) REVERT: C 520 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8327 (pt) REVERT: C 541 ASP cc_start: 0.9213 (m-30) cc_final: 0.8960 (t0) REVERT: C 563 PHE cc_start: 0.3232 (OUTLIER) cc_final: 0.2316 (m-10) REVERT: C 730 MET cc_start: 0.9722 (mtp) cc_final: 0.9291 (ptp) REVERT: D 429 MET cc_start: 0.8367 (mpp) cc_final: 0.7989 (mpp) REVERT: D 436 MET cc_start: 0.9393 (ptm) cc_final: 0.9193 (ppp) REVERT: D 485 MET cc_start: 0.9075 (mtm) cc_final: 0.8495 (mtt) REVERT: D 696 MET cc_start: 0.9253 (mmt) cc_final: 0.8983 (mmm) REVERT: D 773 LEU cc_start: 0.9787 (OUTLIER) cc_final: 0.9509 (tp) REVERT: D 785 LYS cc_start: 0.9545 (tttt) cc_final: 0.9307 (tppt) REVERT: H 117 MET cc_start: 0.9563 (mmp) cc_final: 0.9335 (tpt) REVERT: H 120 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9173 (pp) REVERT: H 189 ILE cc_start: 0.9546 (mm) cc_final: 0.9161 (tt) REVERT: H 191 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9095 (mm-30) REVERT: F 10 MET cc_start: 0.8851 (ttt) cc_final: 0.7954 (tmm) REVERT: F 31 ASP cc_start: 0.8713 (m-30) cc_final: 0.8340 (m-30) REVERT: F 160 ASN cc_start: 0.8991 (t0) cc_final: 0.8740 (t0) REVERT: F 200 MET cc_start: 0.9683 (ttp) cc_final: 0.9450 (mtm) REVERT: G 12 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9465 (mm) REVERT: G 63 LEU cc_start: 0.9210 (mt) cc_final: 0.8987 (pt) REVERT: G 117 MET cc_start: 0.9237 (mtm) cc_final: 0.8986 (tpt) REVERT: G 206 LYS cc_start: 0.8993 (mmtp) cc_final: 0.8488 (mmtp) REVERT: E 58 MET cc_start: 0.8171 (pmm) cc_final: 0.7870 (pmm) REVERT: E 117 MET cc_start: 0.9262 (tpp) cc_final: 0.8381 (tpt) REVERT: E 121 CYS cc_start: 0.8943 (m) cc_final: 0.8209 (m) REVERT: E 149 ASN cc_start: 0.9695 (t0) cc_final: 0.9318 (t0) REVERT: E 151 ILE cc_start: 0.9854 (mm) cc_final: 0.9639 (tp) outliers start: 44 outliers final: 29 residues processed: 256 average time/residue: 0.1119 time to fit residues: 46.3253 Evaluate side-chains 250 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.064900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.048819 restraints weight = 94632.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050228 restraints weight = 53354.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051236 restraints weight = 36740.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051830 restraints weight = 28200.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052360 restraints weight = 23849.228| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18530 Z= 0.124 Angle : 0.647 11.278 25042 Z= 0.318 Chirality : 0.043 0.250 2800 Planarity : 0.004 0.057 3056 Dihedral : 7.984 111.678 2596 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 1.56 % Allowed : 17.88 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2256 helix: 2.09 (0.15), residues: 1269 sheet: -1.40 (0.37), residues: 191 loop : -0.49 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 683 TYR 0.028 0.001 TYR F 156 PHE 0.035 0.001 PHE D 553 TRP 0.009 0.001 TRP H 33 HIS 0.002 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00271 (18516) covalent geometry : angle 0.64732 (25020) SS BOND : bond 0.00161 ( 11) SS BOND : angle 0.36498 ( 22) hydrogen bonds : bond 0.03367 ( 1060) hydrogen bonds : angle 4.17155 ( 3033) Misc. bond : bond 0.00944 ( 3) *********************** 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 265 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 MET cc_start: 0.9400 (mpp) cc_final: 0.9005 (ppp) REVERT: A 485 MET cc_start: 0.8837 (mtm) cc_final: 0.8495 (mtt) REVERT: A 736 GLN cc_start: 0.9630 (mm-40) cc_final: 0.9110 (mt0) REVERT: A 770 LEU cc_start: 0.9318 (mm) cc_final: 0.9036 (mm) REVERT: A 819 TYR cc_start: 0.8999 (m-80) cc_final: 0.8402 (m-80) REVERT: A 820 ILE cc_start: 0.9242 (tt) cc_final: 0.8941 (tp) REVERT: B 463 LYS cc_start: 0.9657 (ptpt) cc_final: 0.9433 (tptt) REVERT: B 485 MET cc_start: 0.9483 (mtm) cc_final: 0.8860 (mtm) REVERT: B 525 MET cc_start: 0.8360 (tmm) cc_final: 0.7718 (tpp) REVERT: B 607 MET cc_start: 0.9338 (mmt) cc_final: 0.8811 (mmm) REVERT: B 608 GLN cc_start: 0.9088 (mp10) cc_final: 0.8828 (mp10) REVERT: B 641 ASN cc_start: 0.8639 (t0) cc_final: 0.8293 (t0) REVERT: B 690 GLU cc_start: 0.9469 (OUTLIER) cc_final: 0.9168 (mt-10) REVERT: B 696 MET cc_start: 0.8917 (tpt) cc_final: 0.8558 (tpp) REVERT: B 743 MET cc_start: 0.9091 (ppp) cc_final: 0.8649 (ppp) REVERT: C 472 TYR cc_start: 0.9017 (m-80) cc_final: 0.8389 (m-80) REVERT: C 485 MET cc_start: 0.8277 (mtm) cc_final: 0.7618 (mtm) REVERT: C 518 MET cc_start: 0.9224 (mtp) cc_final: 0.8890 (mtm) REVERT: C 520 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8329 (pt) REVERT: C 563 PHE cc_start: 0.3140 (OUTLIER) cc_final: 0.2278 (m-10) REVERT: C 730 MET cc_start: 0.9701 (mtp) cc_final: 0.9270 (ptp) REVERT: D 429 MET cc_start: 0.8264 (mpp) cc_final: 0.7898 (mpp) REVERT: D 485 MET cc_start: 0.9064 (mtm) cc_final: 0.8479 (mtt) REVERT: D 558 VAL cc_start: 0.9535 (t) cc_final: 0.9302 (p) REVERT: D 636 SER cc_start: 0.9768 (m) cc_final: 0.9492 (p) REVERT: D 696 MET cc_start: 0.9244 (mmt) cc_final: 0.8972 (mmm) REVERT: D 785 LYS cc_start: 0.9510 (tttt) cc_final: 0.9256 (tppt) REVERT: H 117 MET cc_start: 0.9525 (mmp) cc_final: 0.9321 (tpt) REVERT: H 120 LEU cc_start: 0.9377 (tt) cc_final: 0.9174 (pp) REVERT: H 189 ILE cc_start: 0.9550 (mm) cc_final: 0.9165 (tt) REVERT: F 10 MET cc_start: 0.8830 (ttt) cc_final: 0.7928 (tmm) REVERT: F 31 ASP cc_start: 0.8689 (m-30) cc_final: 0.8304 (m-30) REVERT: F 200 MET cc_start: 0.9682 (ttp) cc_final: 0.9453 (mtm) REVERT: G 117 MET cc_start: 0.9228 (mtm) cc_final: 0.8979 (tpt) REVERT: G 206 LYS cc_start: 0.9002 (mmtp) cc_final: 0.8468 (mmtp) REVERT: E 58 MET cc_start: 0.8086 (pmm) cc_final: 0.7680 (pmm) REVERT: E 114 LEU cc_start: 0.9286 (mt) cc_final: 0.9005 (mp) REVERT: E 117 MET cc_start: 0.9227 (tpp) cc_final: 0.8325 (tpt) REVERT: E 121 CYS cc_start: 0.8912 (m) cc_final: 0.8241 (m) REVERT: E 151 ILE cc_start: 0.9851 (mm) cc_final: 0.9623 (tp) outliers start: 30 outliers final: 24 residues processed: 253 average time/residue: 0.1109 time to fit residues: 45.5236 Evaluate side-chains 245 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 550 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 641 ASN F 160 ASN G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.063809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.047757 restraints weight = 95424.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049158 restraints weight = 53991.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050139 restraints weight = 37090.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050803 restraints weight = 28725.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051156 restraints weight = 24075.807| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18530 Z= 0.170 Angle : 0.671 15.041 25042 Z= 0.334 Chirality : 0.043 0.228 2800 Planarity : 0.004 0.055 3056 Dihedral : 7.916 110.300 2596 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.43 % Rotamer: Outliers : 1.92 % Allowed : 17.98 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 2256 helix: 1.97 (0.15), residues: 1278 sheet: -1.30 (0.38), residues: 194 loop : -0.56 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 683 TYR 0.024 0.001 TYR F 156 PHE 0.033 0.001 PHE D 553 TRP 0.017 0.001 TRP H 33 HIS 0.003 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00374 (18516) covalent geometry : angle 0.67097 (25020) SS BOND : bond 0.00203 ( 11) SS BOND : angle 0.32920 ( 22) hydrogen bonds : bond 0.03458 ( 1060) hydrogen bonds : angle 4.29712 ( 3033) Misc. bond : bond 0.00933 ( 3) *********************** 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 256 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.501 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 436 MET cc_start: 0.9441 (mpp) cc_final: 0.9044 (ppp) REVERT: A 485 MET cc_start: 0.8808 (mtm) cc_final: 0.8485 (mtt) REVERT: A 736 GLN cc_start: 0.9624 (mm-40) cc_final: 0.9110 (mp10) REVERT: A 820 ILE cc_start: 0.9271 (tt) cc_final: 0.8969 (tp) REVERT: B 463 LYS cc_start: 0.9668 (ptpt) cc_final: 0.9442 (tptt) REVERT: B 485 MET cc_start: 0.9493 (mtm) cc_final: 0.8865 (mtm) REVERT: B 525 MET cc_start: 0.8345 (tmm) cc_final: 0.7699 (tpp) REVERT: B 607 MET cc_start: 0.9396 (mmt) cc_final: 0.8773 (mmm) REVERT: B 608 GLN cc_start: 0.9152 (mp10) cc_final: 0.8863 (mp10) REVERT: B 641 ASN cc_start: 0.8661 (t0) cc_final: 0.8324 (t0) REVERT: B 690 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9109 (mt-10) REVERT: B 696 MET cc_start: 0.9000 (tpt) cc_final: 0.8631 (tpp) REVERT: B 743 MET cc_start: 0.9098 (ppp) cc_final: 0.8644 (ppp) REVERT: B 829 MET cc_start: 0.8837 (mtm) cc_final: 0.8560 (mtm) REVERT: C 472 TYR cc_start: 0.9035 (m-80) cc_final: 0.8375 (m-80) REVERT: C 485 MET cc_start: 0.8301 (mtm) cc_final: 0.7491 (mtm) REVERT: C 518 MET cc_start: 0.9292 (mtp) cc_final: 0.8917 (mtm) REVERT: C 520 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8374 (pt) REVERT: C 563 PHE cc_start: 0.3344 (OUTLIER) cc_final: 0.2388 (m-10) REVERT: C 730 MET cc_start: 0.9696 (mtp) cc_final: 0.9239 (ptp) REVERT: D 429 MET cc_start: 0.8310 (mpp) cc_final: 0.7939 (mpp) REVERT: D 436 MET cc_start: 0.9413 (ppp) cc_final: 0.9178 (ppp) REVERT: D 485 MET cc_start: 0.9091 (mtm) cc_final: 0.8502 (mtt) REVERT: D 525 MET cc_start: 0.8258 (tpp) cc_final: 0.7899 (tpp) REVERT: D 636 SER cc_start: 0.9753 (m) cc_final: 0.9506 (p) REVERT: D 696 MET cc_start: 0.9276 (mmt) cc_final: 0.9016 (mmm) REVERT: D 726 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9266 (pp) REVERT: D 735 GLU cc_start: 0.9504 (tt0) cc_final: 0.8997 (tm-30) REVERT: D 773 LEU cc_start: 0.9800 (OUTLIER) cc_final: 0.9502 (tp) REVERT: D 785 LYS cc_start: 0.9510 (tttt) cc_final: 0.9275 (tppt) REVERT: H 117 MET cc_start: 0.9525 (mmp) cc_final: 0.9313 (tpt) REVERT: H 189 ILE cc_start: 0.9546 (mm) cc_final: 0.9169 (tt) REVERT: F 10 MET cc_start: 0.8893 (ttt) cc_final: 0.7968 (tmm) REVERT: F 31 ASP cc_start: 0.8795 (m-30) cc_final: 0.8316 (m-30) REVERT: F 200 MET cc_start: 0.9665 (ttp) cc_final: 0.9433 (mtm) REVERT: G 12 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9471 (mm) REVERT: G 117 MET cc_start: 0.9281 (mtm) cc_final: 0.9006 (tpt) REVERT: G 206 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8505 (mmtp) REVERT: E 58 MET cc_start: 0.8011 (pmm) cc_final: 0.7548 (pmm) REVERT: E 114 LEU cc_start: 0.9303 (mt) cc_final: 0.9022 (mp) REVERT: E 117 MET cc_start: 0.9220 (tpp) cc_final: 0.8341 (tpt) REVERT: E 121 CYS cc_start: 0.8936 (m) cc_final: 0.8289 (m) outliers start: 37 outliers final: 28 residues processed: 244 average time/residue: 0.1065 time to fit residues: 41.9573 Evaluate side-chains 248 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 641 ASN G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.062903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.046678 restraints weight = 97824.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.047966 restraints weight = 56008.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.048902 restraints weight = 39433.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049573 restraints weight = 30701.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.049966 restraints weight = 25953.668| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 18530 Z= 0.222 Angle : 0.714 12.908 25042 Z= 0.359 Chirality : 0.044 0.207 2800 Planarity : 0.004 0.057 3056 Dihedral : 7.925 109.761 2596 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 1.92 % Allowed : 18.04 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % 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: 1.01 (0.19), residues: 2256 helix: 1.81 (0.15), residues: 1278 sheet: -1.31 (0.37), residues: 201 loop : -0.65 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 683 TYR 0.028 0.001 TYR F 156 PHE 0.037 0.002 PHE D 553 TRP 0.018 0.001 TRP H 33 HIS 0.003 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00479 (18516) covalent geometry : angle 0.71426 (25020) SS BOND : bond 0.00255 ( 11) SS BOND : angle 0.40426 ( 22) hydrogen bonds : bond 0.03748 ( 1060) hydrogen bonds : angle 4.49530 ( 3033) Misc. bond : bond 0.00934 ( 3) ********************** 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 244 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.8388 (mpp) cc_final: 0.7912 (mpp) REVERT: A 485 MET cc_start: 0.8756 (mtm) cc_final: 0.8498 (mtt) REVERT: A 736 GLN cc_start: 0.9610 (mm-40) cc_final: 0.9066 (mp10) REVERT: A 819 TYR cc_start: 0.8878 (m-80) cc_final: 0.8304 (m-80) REVERT: A 820 ILE cc_start: 0.9390 (tt) cc_final: 0.9077 (tp) REVERT: B 463 LYS cc_start: 0.9664 (ptpt) cc_final: 0.9430 (tptt) REVERT: B 485 MET cc_start: 0.9475 (mtm) cc_final: 0.8827 (mtm) REVERT: B 525 MET cc_start: 0.8361 (tmm) cc_final: 0.7729 (tpp) REVERT: B 607 MET cc_start: 0.9407 (mmt) cc_final: 0.8685 (mmm) REVERT: B 641 ASN cc_start: 0.8637 (t0) cc_final: 0.8293 (t0) REVERT: B 690 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9076 (mt-10) REVERT: B 696 MET cc_start: 0.9030 (tpt) cc_final: 0.8671 (tpp) REVERT: B 743 MET cc_start: 0.9089 (ppp) cc_final: 0.8598 (ppp) REVERT: B 829 MET cc_start: 0.8769 (mtm) cc_final: 0.8561 (mtm) REVERT: C 472 TYR cc_start: 0.9003 (m-80) cc_final: 0.8430 (m-80) REVERT: C 485 MET cc_start: 0.8359 (mtm) cc_final: 0.7930 (mtm) REVERT: C 518 MET cc_start: 0.9325 (mtp) cc_final: 0.8971 (mtp) REVERT: C 520 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8439 (pt) REVERT: C 563 PHE cc_start: 0.3506 (OUTLIER) cc_final: 0.2503 (m-10) REVERT: C 730 MET cc_start: 0.9717 (mtp) cc_final: 0.9281 (ptp) REVERT: D 429 MET cc_start: 0.8344 (mpp) cc_final: 0.7969 (mpp) REVERT: D 436 MET cc_start: 0.9425 (ppp) cc_final: 0.9197 (ppp) REVERT: D 485 MET cc_start: 0.9134 (mtm) cc_final: 0.8555 (mtt) REVERT: D 525 MET cc_start: 0.8193 (tpp) cc_final: 0.7807 (tpp) REVERT: D 550 CYS cc_start: 0.9097 (m) cc_final: 0.8803 (t) REVERT: D 553 PHE cc_start: 0.9292 (m-80) cc_final: 0.9072 (m-80) REVERT: D 726 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9229 (pp) REVERT: D 735 GLU cc_start: 0.9509 (tt0) cc_final: 0.9004 (tm-30) REVERT: H 189 ILE cc_start: 0.9572 (mm) cc_final: 0.9163 (tt) REVERT: F 200 MET cc_start: 0.9664 (ttp) cc_final: 0.9387 (mtm) REVERT: G 12 LEU cc_start: 0.9817 (OUTLIER) cc_final: 0.9523 (mm) REVERT: G 117 MET cc_start: 0.9314 (mtm) cc_final: 0.9006 (tpt) REVERT: G 206 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8607 (mmtt) REVERT: E 58 MET cc_start: 0.7986 (pmm) cc_final: 0.7460 (pmm) REVERT: E 70 GLU cc_start: 0.8718 (pt0) cc_final: 0.8417 (pt0) REVERT: E 114 LEU cc_start: 0.9334 (mt) cc_final: 0.9049 (mp) REVERT: E 117 MET cc_start: 0.9207 (tpp) cc_final: 0.8318 (tpt) REVERT: E 121 CYS cc_start: 0.8935 (m) cc_final: 0.8281 (m) outliers start: 37 outliers final: 31 residues processed: 234 average time/residue: 0.1097 time to fit residues: 41.5170 Evaluate side-chains 240 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.064170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.047862 restraints weight = 97260.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.049233 restraints weight = 55310.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050195 restraints weight = 38500.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.050892 restraints weight = 30116.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051233 restraints weight = 25275.501| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18530 Z= 0.152 Angle : 0.688 12.427 25042 Z= 0.337 Chirality : 0.044 0.235 2800 Planarity : 0.004 0.055 3056 Dihedral : 7.656 109.987 2596 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 1.98 % Allowed : 18.04 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % 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: 1.12 (0.19), residues: 2256 helix: 1.89 (0.15), residues: 1276 sheet: -1.38 (0.37), residues: 194 loop : -0.57 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 683 TYR 0.024 0.001 TYR F 156 PHE 0.036 0.001 PHE D 553 TRP 0.014 0.001 TRP H 33 HIS 0.002 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00338 (18516) covalent geometry : angle 0.68782 (25020) SS BOND : bond 0.00176 ( 11) SS BOND : angle 0.36636 ( 22) hydrogen bonds : bond 0.03519 ( 1060) hydrogen bonds : angle 4.33465 ( 3033) Misc. bond : bond 0.00933 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.53 seconds wall clock time: 49 minutes 39.19 seconds (2979.19 seconds total)