Starting phenix.real_space_refine on Thu Feb 5 15:51:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9c_71406/02_2026/9p9c_71406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9c_71406/02_2026/9p9c_71406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p9c_71406/02_2026/9p9c_71406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9c_71406/02_2026/9p9c_71406.map" model { file = "/net/cci-nas-00/data/ceres_data/9p9c_71406/02_2026/9p9c_71406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9c_71406/02_2026/9p9c_71406.cif" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 132 5.16 5 Cl 4 4.86 5 C 11796 2.51 5 N 2916 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18100 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 388} 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': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 1 Chain: "D" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Chain: "H" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "F" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "G" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Time building chain proxies: 4.41, per 1000 atoms: 0.24 Number of scatterers: 18100 At special positions: 0 Unit cell: (128.34, 111.6, 134.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 132 16.00 O 3252 8.00 N 2916 7.00 C 11796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 797.0 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: 94 helices and 26 sheets defined 59.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 433 through 437 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: 3.666A pdb=" N TRP A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 608 Processing helix chain 'A' and resid 617 through 647 Processing helix chain 'A' and resid 657 through 664 removed outlier: 3.594A pdb=" N LEU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) 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 737 Processing helix chain 'A' and resid 764 through 779 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 840 removed outlier: 3.655A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 544 through 568 removed outlier: 3.842A pdb=" N PHE B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 removed outlier: 3.694A pdb=" N SER B 598 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 640 Processing helix chain 'B' and resid 641 through 648 removed outlier: 3.525A pdb=" N PHE B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 removed outlier: 3.709A pdb=" N LYS B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 684 removed outlier: 3.949A pdb=" N GLU B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 698 Processing helix chain 'B' and resid 707 through 717 removed outlier: 3.541A pdb=" N GLY B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 736 removed outlier: 3.891A pdb=" N GLN B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 814 through 839 removed outlier: 3.645A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 445 through 459 Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.527A pdb=" N GLU C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 546 through 568 Processing helix chain 'C' and resid 594 through 607 removed outlier: 3.801A pdb=" N SER C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 648 removed outlier: 4.044A pdb=" N VAL C 648 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 675 through 683 Processing helix chain 'C' and resid 686 through 699 Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.655A pdb=" N GLU C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 737 " --> pdb=" O TYR C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 778 Processing helix chain 'C' and resid 779 through 790 Processing helix chain 'C' and resid 796 through 800 removed outlier: 3.985A pdb=" N ASP C 799 " --> pdb=" O GLY C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 840 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 Processing helix chain 'D' and resid 594 through 608 Processing helix chain 'D' and resid 617 through 640 Processing helix chain 'D' and resid 657 through 664 removed outlier: 3.638A pdb=" N LEU D 661 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 683 removed outlier: 3.913A pdb=" N GLU D 679 " --> pdb=" O GLY D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 698 Processing helix chain 'D' and resid 707 through 718 removed outlier: 4.115A pdb=" N VAL D 715 " --> pdb=" O GLY D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 736 Processing helix chain 'D' and resid 764 through 779 Processing helix chain 'D' and resid 779 through 791 Processing helix chain 'D' and resid 810 through 813 Processing helix chain 'D' and resid 814 through 840 removed outlier: 4.283A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 29 Processing helix chain 'H' and resid 95 through 105 Processing helix chain 'H' and resid 105 through 127 removed outlier: 3.742A pdb=" N ILE H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 161 removed outlier: 4.091A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 210 removed outlier: 3.527A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR H 209 " --> pdb=" O HIS H 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 125 removed outlier: 3.978A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 3.541A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 206 removed outlier: 3.751A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE F 182 " --> pdb=" O TRP F 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 7 through 29 removed outlier: 3.718A 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 124 Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.718A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 210 removed outlier: 3.655A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 29 removed outlier: 4.089A pdb=" N LEU E 11 " --> pdb=" O GLY E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 105 through 126 removed outlier: 3.618A pdb=" N ILE E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 4.090A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.864A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 464 through 466 removed outlier: 6.286A pdb=" N VAL A 419 " --> 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 519 through 520 Processing sheet with id=AA5, first strand: chain 'A' and resid 668 through 670 removed outlier: 6.770A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 462 through 466 removed outlier: 6.439A pdb=" N VAL B 417 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA B 465 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL B 419 " --> pdb=" O ALA B 465 " (cutoff:3.500A) 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 removed outlier: 3.544A pdb=" N ASP B 512 " --> pdb=" O THR B 758 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 758 " --> pdb=" O ASP B 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 518 through 521 removed outlier: 3.905A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 527 removed outlier: 4.080A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 668 through 670 removed outlier: 5.866A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 464 through 466 removed outlier: 5.345A pdb=" N VAL C 419 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB5, first strand: chain 'C' and resid 511 through 513 Processing sheet with id=AB6, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.758A pdb=" N MET C 518 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 726 through 727 removed outlier: 3.678A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 668 through 670 removed outlier: 6.475A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 462 through 466 removed outlier: 5.778A pdb=" N VAL D 417 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA D 465 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL D 419 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 496 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AC2, first strand: chain 'D' and resid 511 through 513 Processing sheet with id=AC3, first strand: chain 'D' and resid 518 through 520 removed outlier: 4.361A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 668 through 670 removed outlier: 6.277A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU D 725 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N PHE D 722 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS D 527 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 34 through 36 removed outlier: 4.265A pdb=" N MET H 58 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 69 " --> pdb=" O MET H 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS H 60 " --> pdb=" O CYS H 67 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU H 76 " --> pdb=" O CYS H 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.966A pdb=" N LEU F 76 " --> pdb=" O CYS F 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 36 Processing sheet with id=AC8, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.596A pdb=" N HIS E 60 " --> pdb=" O CYS E 67 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 3027 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: 3.59 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.19: 16 1.19 - 1.35: 5495 1.35 - 1.51: 5902 1.51 - 1.68: 6883 1.68 - 1.84: 220 Bond restraints: 18516 Sorted by residual: bond pdb=" C4 CYZ D 901 " pdb=" C5 CYZ D 901 " ideal model delta sigma weight residual 1.512 1.021 0.491 2.00e-02 2.50e+03 6.02e+02 bond pdb=" C5 CYZ B 901 " pdb=" C6 CYZ B 901 " ideal model delta sigma weight residual 1.553 1.063 0.490 2.00e-02 2.50e+03 6.00e+02 bond pdb=" C4 CYZ C 901 " pdb=" C5 CYZ C 901 " ideal model delta sigma weight residual 1.512 1.022 0.490 2.00e-02 2.50e+03 6.00e+02 bond pdb=" C4 CYZ A 901 " pdb=" C5 CYZ A 901 " ideal model delta sigma weight residual 1.512 1.022 0.490 2.00e-02 2.50e+03 6.00e+02 bond pdb=" C4 CYZ B 901 " pdb=" C5 CYZ B 901 " ideal model delta sigma weight residual 1.512 1.022 0.490 2.00e-02 2.50e+03 6.00e+02 ... (remaining 18511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 24897 3.63 - 7.27: 95 7.27 - 10.90: 12 10.90 - 14.53: 5 14.53 - 18.17: 11 Bond angle restraints: 25020 Sorted by residual: angle pdb=" C1 CYZ D 901 " pdb=" C2 CYZ D 901 " pdb=" C3 CYZ D 901 " ideal model delta sigma weight residual 106.92 125.09 -18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" C1 CYZ B 901 " pdb=" C2 CYZ B 901 " pdb=" C3 CYZ B 901 " ideal model delta sigma weight residual 106.92 124.47 -17.55 3.00e+00 1.11e-01 3.42e+01 angle pdb=" C1 CYZ A 901 " pdb=" C2 CYZ A 901 " pdb=" C3 CYZ A 901 " ideal model delta sigma weight residual 106.92 124.26 -17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" O3 CYZ D 901 " pdb=" S2 CYZ D 901 " pdb=" O4 CYZ D 901 " ideal model delta sigma weight residual 118.35 101.09 17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" O3 CYZ B 901 " pdb=" S2 CYZ B 901 " pdb=" O4 CYZ B 901 " ideal model delta sigma weight residual 118.35 101.09 17.26 3.00e+00 1.11e-01 3.31e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 10266 21.17 - 42.34: 568 42.34 - 63.51: 56 63.51 - 84.68: 14 84.68 - 105.85: 9 Dihedral angle restraints: 10913 sinusoidal: 4317 harmonic: 6596 Sorted by residual: dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 -177.59 -89.41 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual -86.00 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CA THR C 806 " pdb=" C THR C 806 " pdb=" N SER C 807 " pdb=" CA SER C 807 " ideal model delta harmonic sigma weight residual -180.00 -143.47 -36.53 0 5.00e+00 4.00e-02 5.34e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.425: 2785 0.425 - 0.850: 7 0.850 - 1.275: 0 1.275 - 1.701: 0 1.701 - 2.126: 8 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C5 CYZ C 901 " pdb=" C4 CYZ C 901 " pdb=" C6 CYZ C 901 " pdb=" C7 CYZ C 901 " both_signs ideal model delta sigma weight residual False 3.31 1.18 2.13 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" C5 CYZ A 901 " pdb=" C4 CYZ A 901 " pdb=" C6 CYZ A 901 " pdb=" C7 CYZ A 901 " both_signs ideal model delta sigma weight residual False 3.31 1.18 2.12 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" C5 CYZ D 901 " pdb=" C4 CYZ D 901 " pdb=" C6 CYZ D 901 " pdb=" C7 CYZ D 901 " both_signs ideal model delta sigma weight residual False 3.31 1.18 2.12 2.00e-01 2.50e+01 1.13e+02 ... (remaining 2797 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 650 " 0.567 9.50e-02 1.11e+02 2.54e-01 3.95e+01 pdb=" NE ARG B 650 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 650 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 650 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 650 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 427 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C TYR C 427 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR C 427 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 428 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 832 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C ALA D 832 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA D 832 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 833 " 0.009 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6314 2.84 - 3.36: 19727 3.36 - 3.87: 30841 3.87 - 4.39: 35184 4.39 - 4.90: 57321 Nonbonded interactions: 149387 Sorted by model distance: nonbonded pdb=" C1 CYZ D 901 " pdb=" C4 CYZ D 901 " model vdw 2.327 3.016 nonbonded pdb=" C1 CYZ C 901 " pdb=" C4 CYZ C 901 " model vdw 2.328 3.016 nonbonded pdb=" C1 CYZ A 901 " pdb=" C4 CYZ A 901 " model vdw 2.332 3.016 nonbonded pdb=" C1 CYZ B 901 " pdb=" C4 CYZ B 901 " model vdw 2.334 3.016 nonbonded pdb=" C3 CYZ B 901 " pdb=" C6 CYZ B 901 " model vdw 2.348 2.992 ... (remaining 149382 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.220 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 0.491 18528 Z= 0.829 Angle : 0.729 18.166 25042 Z= 0.368 Chirality : 0.119 2.126 2800 Planarity : 0.006 0.254 3056 Dihedral : 12.926 105.852 6672 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.10 % Allowed : 0.88 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 2256 helix: 2.29 (0.15), residues: 1286 sheet: -1.96 (0.44), residues: 140 loop : -1.34 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 650 TYR 0.020 0.001 TYR C 838 PHE 0.023 0.001 PHE C 645 TRP 0.020 0.001 TRP G 178 HIS 0.004 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.01644 (18516) covalent geometry : angle 0.72915 (25020) SS BOND : bond 0.00165 ( 11) SS BOND : angle 0.46599 ( 22) hydrogen bonds : bond 0.12397 ( 1043) hydrogen bonds : angle 5.54725 ( 3027) Misc. bond : bond 0.04189 ( 1) *********************** 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 618 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 616 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: 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 518 MET cc_start: 0.9156 (ttm) cc_final: 0.8753 (tpp) REVERT: A 525 MET cc_start: 0.9068 (ttm) cc_final: 0.8568 (tmm) REVERT: A 531 LYS cc_start: 0.7469 (tppp) cc_final: 0.6502 (pptt) REVERT: A 673 ASP cc_start: 0.9151 (t0) cc_final: 0.8584 (p0) REVERT: B 512 ASP cc_start: 0.7982 (m-30) cc_final: 0.7578 (m-30) REVERT: B 525 MET cc_start: 0.9071 (ttm) cc_final: 0.8740 (tmm) REVERT: B 541 ASP cc_start: 0.8912 (m-30) cc_final: 0.8505 (t0) REVERT: B 548 TRP cc_start: 0.9380 (m100) cc_final: 0.8917 (m100) REVERT: B 692 MET cc_start: 0.9385 (mtp) cc_final: 0.9112 (mtp) REVERT: B 730 MET cc_start: 0.9005 (mpp) cc_final: 0.8753 (mpp) REVERT: B 732 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8777 (tp30) REVERT: B 819 TYR cc_start: 0.9283 (m-10) cc_final: 0.8943 (m-80) REVERT: C 423 MET cc_start: 0.8819 (mmm) cc_final: 0.7768 (mmm) REVERT: C 440 ASN cc_start: 0.8845 (m-40) cc_final: 0.8402 (m-40) REVERT: C 518 MET cc_start: 0.9162 (ttm) cc_final: 0.8867 (mtm) REVERT: C 525 MET cc_start: 0.9120 (ttm) cc_final: 0.8344 (tpp) REVERT: C 608 GLN cc_start: 0.8784 (tp40) cc_final: 0.8535 (tp40) REVERT: C 638 TYR cc_start: 0.9237 (t80) cc_final: 0.8974 (t80) REVERT: C 730 MET cc_start: 0.9151 (mpp) cc_final: 0.8691 (mpp) REVERT: C 750 ASP cc_start: 0.8814 (p0) cc_final: 0.8567 (p0) REVERT: C 785 LYS cc_start: 0.9635 (tttt) cc_final: 0.9326 (tptp) REVERT: C 818 PHE cc_start: 0.9401 (m-80) cc_final: 0.8731 (m-80) REVERT: D 472 TYR cc_start: 0.7504 (m-80) cc_final: 0.7250 (m-80) REVERT: D 525 MET cc_start: 0.8605 (ttm) cc_final: 0.8321 (tpp) REVERT: D 609 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7529 (tp40) REVERT: D 743 MET cc_start: 0.9478 (ptm) cc_final: 0.8826 (ptm) REVERT: D 748 ASN cc_start: 0.9198 (m-40) cc_final: 0.8846 (t0) REVERT: D 769 ASN cc_start: 0.9516 (t0) cc_final: 0.9233 (t0) REVERT: H 23 LEU cc_start: 0.9670 (mt) cc_final: 0.9411 (tp) REVERT: H 96 TYR cc_start: 0.8590 (t80) cc_final: 0.8298 (t80) REVERT: H 156 TYR cc_start: 0.9466 (t80) cc_final: 0.9177 (t80) REVERT: H 160 ASN cc_start: 0.9047 (m-40) cc_final: 0.8581 (m110) REVERT: H 182 PHE cc_start: 0.8847 (m-10) cc_final: 0.8627 (m-80) REVERT: H 203 ASP cc_start: 0.9032 (t0) cc_final: 0.8831 (t70) REVERT: F 81 ASP cc_start: 0.8620 (t0) cc_final: 0.8284 (t0) REVERT: F 110 LEU cc_start: 0.9623 (mt) cc_final: 0.9418 (mt) REVERT: F 117 MET cc_start: 0.9155 (mmm) cc_final: 0.8851 (mmp) REVERT: G 33 TRP cc_start: 0.9459 (m100) cc_final: 0.8982 (m100) REVERT: G 181 TYR cc_start: 0.9305 (m-80) cc_final: 0.8762 (m-80) REVERT: G 200 MET cc_start: 0.9399 (mtm) cc_final: 0.9197 (mtm) REVERT: G 205 HIS cc_start: 0.8492 (t-90) cc_final: 0.8191 (t-90) REVERT: E 13 THR cc_start: 0.9566 (m) cc_final: 0.9305 (p) REVERT: E 142 PHE cc_start: 0.9364 (m-80) cc_final: 0.9131 (m-10) REVERT: E 182 PHE cc_start: 0.8978 (m-80) cc_final: 0.8620 (m-10) REVERT: E 200 MET cc_start: 0.9280 (mtm) cc_final: 0.8897 (mtp) REVERT: E 203 ASP cc_start: 0.9231 (t0) cc_final: 0.8690 (t0) outliers start: 2 outliers final: 1 residues processed: 616 average time/residue: 0.1454 time to fit residues: 134.6809 Evaluate side-chains 347 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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: 0.7980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN C 609 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** 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 = 0.3519 r_free = 0.3519 target = 0.072830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056100 restraints weight = 89571.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057720 restraints weight = 52451.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.058815 restraints weight = 36293.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059614 restraints weight = 28125.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060059 restraints weight = 23450.877| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18528 Z= 0.280 Angle : 0.679 7.584 25042 Z= 0.364 Chirality : 0.044 0.170 2800 Planarity : 0.005 0.058 3056 Dihedral : 7.397 109.948 2596 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.21 % Allowed : 3.90 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2256 helix: 1.78 (0.14), residues: 1295 sheet: -1.67 (0.43), residues: 145 loop : -1.26 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 737 TYR 0.023 0.002 TYR A 838 PHE 0.021 0.002 PHE D 836 TRP 0.029 0.002 TRP G 178 HIS 0.013 0.002 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00600 (18516) covalent geometry : angle 0.67804 (25020) SS BOND : bond 0.00456 ( 11) SS BOND : angle 1.22106 ( 22) hydrogen bonds : bond 0.04324 ( 1043) hydrogen bonds : angle 4.98231 ( 3027) Misc. bond : bond 0.00173 ( 1) *********************** 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 410 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 406 time to evaluate : 0.661 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: A 525 MET cc_start: 0.8812 (ttm) cc_final: 0.8184 (tmm) REVERT: A 541 ASP cc_start: 0.9088 (m-30) cc_final: 0.8830 (m-30) REVERT: A 593 PHE cc_start: 0.3056 (m-80) cc_final: 0.2325 (m-80) REVERT: A 673 ASP cc_start: 0.9181 (t0) cc_final: 0.8595 (p0) REVERT: B 525 MET cc_start: 0.9013 (ttm) cc_final: 0.8459 (tmm) REVERT: B 541 ASP cc_start: 0.8883 (m-30) cc_final: 0.8537 (t70) REVERT: B 618 LEU cc_start: 0.9416 (tt) cc_final: 0.9155 (mp) REVERT: B 676 SER cc_start: 0.8675 (p) cc_final: 0.8372 (m) REVERT: B 681 PHE cc_start: 0.9180 (m-80) cc_final: 0.8869 (m-80) REVERT: B 736 GLN cc_start: 0.9431 (mp10) cc_final: 0.8461 (mp10) REVERT: B 819 TYR cc_start: 0.9354 (m-10) cc_final: 0.8967 (m-80) REVERT: C 429 MET cc_start: 0.8749 (mpp) cc_final: 0.8501 (mpp) REVERT: C 525 MET cc_start: 0.9104 (ttm) cc_final: 0.8149 (tmm) REVERT: C 613 ILE cc_start: 0.8983 (tt) cc_final: 0.8601 (tp) REVERT: C 641 ASN cc_start: 0.9049 (t0) cc_final: 0.8783 (t0) REVERT: C 730 MET cc_start: 0.9327 (mpp) cc_final: 0.8976 (mmm) REVERT: D 525 MET cc_start: 0.8545 (ttm) cc_final: 0.8299 (tmm) REVERT: D 549 MET cc_start: 0.8729 (tpt) cc_final: 0.8243 (tpp) REVERT: D 641 ASN cc_start: 0.9381 (t0) cc_final: 0.9151 (t0) REVERT: D 748 ASN cc_start: 0.9214 (m-40) cc_final: 0.8919 (t0) REVERT: D 769 ASN cc_start: 0.9534 (t0) cc_final: 0.9268 (t0) REVERT: D 784 LEU cc_start: 0.9679 (mt) cc_final: 0.9382 (tp) REVERT: H 96 TYR cc_start: 0.8529 (t80) cc_final: 0.8229 (t80) REVERT: H 203 ASP cc_start: 0.8953 (t0) cc_final: 0.8731 (t70) REVERT: F 96 TYR cc_start: 0.8490 (t80) cc_final: 0.8254 (t80) REVERT: F 110 LEU cc_start: 0.9656 (mt) cc_final: 0.9450 (mt) REVERT: F 117 MET cc_start: 0.9184 (mmm) cc_final: 0.8924 (mmp) REVERT: G 33 TRP cc_start: 0.9435 (m100) cc_final: 0.9053 (m100) REVERT: G 181 TYR cc_start: 0.9200 (m-80) cc_final: 0.8815 (m-80) REVERT: E 13 THR cc_start: 0.9669 (m) cc_final: 0.9360 (p) REVERT: E 149 ASN cc_start: 0.9281 (t0) cc_final: 0.9046 (t0) REVERT: E 182 PHE cc_start: 0.8883 (m-80) cc_final: 0.8485 (m-10) REVERT: E 200 MET cc_start: 0.9468 (mtm) cc_final: 0.9106 (mtp) REVERT: E 203 ASP cc_start: 0.9295 (t0) cc_final: 0.8924 (t0) outliers start: 4 outliers final: 1 residues processed: 408 average time/residue: 0.1261 time to fit residues: 80.4733 Evaluate side-chains 290 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 148 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 177 optimal weight: 0.0770 chunk 89 optimal weight: 0.0870 chunk 200 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 ASN B 609 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.075654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059085 restraints weight = 86721.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.060721 restraints weight = 50941.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061867 restraints weight = 35352.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.062672 restraints weight = 27338.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063183 restraints weight = 22770.899| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18528 Z= 0.118 Angle : 0.551 7.273 25042 Z= 0.289 Chirality : 0.042 0.174 2800 Planarity : 0.004 0.086 3056 Dihedral : 7.034 107.633 2596 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2256 helix: 2.05 (0.15), residues: 1302 sheet: -1.19 (0.47), residues: 126 loop : -1.17 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 737 TYR 0.028 0.001 TYR A 838 PHE 0.031 0.001 PHE C 629 TRP 0.028 0.001 TRP D 789 HIS 0.011 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00261 (18516) covalent geometry : angle 0.55026 (25020) SS BOND : bond 0.00187 ( 11) SS BOND : angle 0.81478 ( 22) hydrogen bonds : bond 0.03618 ( 1043) hydrogen bonds : angle 4.35877 ( 3027) Misc. bond : bond 0.00109 ( 1) *********************** 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 424 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 422 time to evaluate : 0.791 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: symmetry clash revert: symmetry clash REVERT: A 478 ASP cc_start: 0.9232 (m-30) cc_final: 0.8779 (p0) REVERT: A 525 MET cc_start: 0.8655 (ttp) cc_final: 0.8137 (tmm) REVERT: A 541 ASP cc_start: 0.9045 (m-30) cc_final: 0.8787 (m-30) REVERT: A 593 PHE cc_start: 0.2978 (m-80) cc_final: 0.2340 (m-80) REVERT: A 673 ASP cc_start: 0.9084 (t0) cc_final: 0.8693 (p0) REVERT: A 681 PHE cc_start: 0.9277 (m-80) cc_final: 0.8942 (m-80) REVERT: B 525 MET cc_start: 0.8960 (ttm) cc_final: 0.8466 (tmm) REVERT: B 541 ASP cc_start: 0.8797 (m-30) cc_final: 0.8527 (t70) REVERT: B 618 LEU cc_start: 0.9326 (tt) cc_final: 0.9101 (mp) REVERT: B 630 PHE cc_start: 0.9309 (t80) cc_final: 0.9088 (t80) REVERT: B 819 TYR cc_start: 0.9214 (m-10) cc_final: 0.8950 (m-80) REVERT: C 518 MET cc_start: 0.8995 (ttm) cc_final: 0.8363 (mtp) REVERT: C 525 MET cc_start: 0.9097 (ttm) cc_final: 0.8102 (tmm) REVERT: C 526 ILE cc_start: 0.9150 (tp) cc_final: 0.8949 (tp) REVERT: C 607 MET cc_start: 0.9126 (mmp) cc_final: 0.8772 (tpp) REVERT: C 613 ILE cc_start: 0.8860 (tt) cc_final: 0.8537 (tp) REVERT: C 638 TYR cc_start: 0.9251 (t80) cc_final: 0.9014 (t80) REVERT: C 641 ASN cc_start: 0.8920 (t0) cc_final: 0.8687 (t0) REVERT: C 730 MET cc_start: 0.9290 (mpp) cc_final: 0.8880 (mpp) REVERT: D 525 MET cc_start: 0.8441 (ttm) cc_final: 0.8204 (tmm) REVERT: D 549 MET cc_start: 0.8403 (tpt) cc_final: 0.7958 (tpp) REVERT: D 551 ILE cc_start: 0.9344 (mm) cc_final: 0.9069 (mm) REVERT: D 748 ASN cc_start: 0.9369 (m-40) cc_final: 0.8872 (t0) REVERT: D 769 ASN cc_start: 0.9497 (t0) cc_final: 0.9201 (t0) REVERT: H 96 TYR cc_start: 0.8451 (t80) cc_final: 0.8231 (t80) REVERT: H 200 MET cc_start: 0.8932 (tpp) cc_final: 0.8690 (tmm) REVERT: H 203 ASP cc_start: 0.8826 (t0) cc_final: 0.8607 (t70) REVERT: F 81 ASP cc_start: 0.8324 (t0) cc_final: 0.8109 (t0) REVERT: F 117 MET cc_start: 0.9105 (mmm) cc_final: 0.8877 (mmp) REVERT: G 32 TYR cc_start: 0.8639 (m-80) cc_final: 0.8125 (m-10) REVERT: G 33 TRP cc_start: 0.9200 (m100) cc_final: 0.8760 (m100) REVERT: G 196 LEU cc_start: 0.9438 (mm) cc_final: 0.9216 (tp) REVERT: G 200 MET cc_start: 0.9117 (mtp) cc_final: 0.8627 (mtt) REVERT: E 13 THR cc_start: 0.9555 (m) cc_final: 0.9305 (p) REVERT: E 33 TRP cc_start: 0.9061 (m100) cc_final: 0.8750 (m-10) REVERT: E 200 MET cc_start: 0.9445 (mtm) cc_final: 0.9181 (mtp) REVERT: E 203 ASP cc_start: 0.9165 (t0) cc_final: 0.8724 (t0) REVERT: E 204 ARG cc_start: 0.8815 (mpt180) cc_final: 0.8435 (mpt180) outliers start: 2 outliers final: 0 residues processed: 423 average time/residue: 0.1318 time to fit residues: 86.5270 Evaluate side-chains 300 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 142 optimal weight: 0.4980 chunk 195 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS ** E 60 HIS ** 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 = 0.3569 r_free = 0.3569 target = 0.075227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058279 restraints weight = 88793.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059951 restraints weight = 51977.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.061125 restraints weight = 35854.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.061931 restraints weight = 27655.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062381 restraints weight = 23031.005| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18528 Z= 0.153 Angle : 0.558 7.483 25042 Z= 0.298 Chirality : 0.042 0.179 2800 Planarity : 0.004 0.048 3056 Dihedral : 6.962 107.434 2596 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % 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: 1.00 (0.19), residues: 2256 helix: 1.92 (0.15), residues: 1298 sheet: -1.35 (0.46), residues: 128 loop : -1.05 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 706 TYR 0.018 0.001 TYR A 669 PHE 0.019 0.001 PHE E 142 TRP 0.022 0.001 TRP H 178 HIS 0.008 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00335 (18516) covalent geometry : angle 0.55757 (25020) SS BOND : bond 0.00249 ( 11) SS BOND : angle 0.82252 ( 22) hydrogen bonds : bond 0.03585 ( 1043) hydrogen bonds : angle 4.38965 ( 3027) Misc. bond : bond 0.00080 ( 1) *********************** 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 395 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 ASP cc_start: 0.9267 (m-30) cc_final: 0.8775 (p0) REVERT: A 518 MET cc_start: 0.8804 (ttt) cc_final: 0.8443 (tpp) REVERT: A 525 MET cc_start: 0.8686 (ttp) cc_final: 0.8210 (tmm) REVERT: A 541 ASP cc_start: 0.9023 (m-30) cc_final: 0.8778 (m-30) REVERT: A 593 PHE cc_start: 0.2869 (m-80) cc_final: 0.2283 (m-80) REVERT: A 673 ASP cc_start: 0.9110 (t0) cc_final: 0.8752 (p0) REVERT: A 681 PHE cc_start: 0.9393 (m-80) cc_final: 0.9029 (m-80) REVERT: A 696 MET cc_start: 0.9121 (mmp) cc_final: 0.8746 (mmm) REVERT: A 743 MET cc_start: 0.8429 (pmm) cc_final: 0.7837 (pmm) REVERT: B 433 ASN cc_start: 0.8673 (t0) cc_final: 0.8383 (t0) REVERT: B 525 MET cc_start: 0.9042 (ttm) cc_final: 0.8757 (tmm) REVERT: B 541 ASP cc_start: 0.8854 (m-30) cc_final: 0.8554 (t70) REVERT: B 608 GLN cc_start: 0.9355 (mm110) cc_final: 0.9082 (mm-40) REVERT: B 618 LEU cc_start: 0.9312 (tt) cc_final: 0.9102 (mp) REVERT: B 630 PHE cc_start: 0.9359 (t80) cc_final: 0.9135 (t80) REVERT: B 676 SER cc_start: 0.8665 (p) cc_final: 0.8349 (m) REVERT: B 681 PHE cc_start: 0.9248 (m-80) cc_final: 0.8985 (m-80) REVERT: B 692 MET cc_start: 0.9352 (mmt) cc_final: 0.8932 (mmm) REVERT: B 733 TYR cc_start: 0.8686 (t80) cc_final: 0.8201 (t80) REVERT: B 810 SER cc_start: 0.8954 (p) cc_final: 0.8598 (p) REVERT: B 819 TYR cc_start: 0.9265 (m-10) cc_final: 0.8904 (m-80) REVERT: C 429 MET cc_start: 0.8501 (mpp) cc_final: 0.8287 (mpp) REVERT: C 485 MET cc_start: 0.8940 (ptp) cc_final: 0.8383 (pmm) REVERT: C 518 MET cc_start: 0.9109 (ttm) cc_final: 0.8441 (mtp) REVERT: C 525 MET cc_start: 0.9156 (ttm) cc_final: 0.8101 (tmm) REVERT: C 613 ILE cc_start: 0.8848 (tt) cc_final: 0.8493 (tp) REVERT: C 638 TYR cc_start: 0.9295 (t80) cc_final: 0.8762 (t80) REVERT: C 641 ASN cc_start: 0.9077 (t0) cc_final: 0.8803 (t0) REVERT: C 730 MET cc_start: 0.9307 (mpp) cc_final: 0.8938 (mpp) REVERT: D 525 MET cc_start: 0.8583 (ttm) cc_final: 0.8251 (tmm) REVERT: D 549 MET cc_start: 0.8360 (tpt) cc_final: 0.7857 (tpp) REVERT: D 551 ILE cc_start: 0.9374 (mm) cc_final: 0.9114 (mm) REVERT: D 748 ASN cc_start: 0.9411 (m-40) cc_final: 0.9015 (t0) REVERT: D 769 ASN cc_start: 0.9522 (t0) cc_final: 0.9262 (t0) REVERT: D 780 VAL cc_start: 0.9703 (t) cc_final: 0.9416 (m) REVERT: D 784 LEU cc_start: 0.9582 (mp) cc_final: 0.9266 (tp) REVERT: H 200 MET cc_start: 0.8974 (tpp) cc_final: 0.8741 (tmm) REVERT: H 203 ASP cc_start: 0.8885 (t0) cc_final: 0.8682 (t70) REVERT: F 96 TYR cc_start: 0.8493 (t80) cc_final: 0.8241 (t80) REVERT: F 110 LEU cc_start: 0.9543 (mt) cc_final: 0.9340 (mt) REVERT: F 117 MET cc_start: 0.9131 (mmm) cc_final: 0.8894 (mmp) REVERT: G 31 ASP cc_start: 0.8198 (p0) cc_final: 0.7366 (p0) REVERT: G 33 TRP cc_start: 0.9360 (m100) cc_final: 0.9049 (m100) REVERT: E 65 ARG cc_start: 0.7208 (tpt-90) cc_final: 0.6642 (ttt90) REVERT: E 149 ASN cc_start: 0.9381 (t0) cc_final: 0.9134 (t0) REVERT: E 203 ASP cc_start: 0.9177 (t0) cc_final: 0.8785 (t0) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1217 time to fit residues: 76.7541 Evaluate side-chains 286 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 199 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.075193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.058411 restraints weight = 89274.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060067 restraints weight = 52886.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061210 restraints weight = 36837.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061987 restraints weight = 28507.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062405 restraints weight = 23846.152| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18528 Z= 0.154 Angle : 0.566 9.924 25042 Z= 0.298 Chirality : 0.042 0.202 2800 Planarity : 0.004 0.036 3056 Dihedral : 6.906 106.787 2596 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % 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: 0.94 (0.19), residues: 2256 helix: 1.83 (0.15), residues: 1300 sheet: -1.36 (0.45), residues: 124 loop : -1.02 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 737 TYR 0.022 0.001 TYR G 32 PHE 0.028 0.001 PHE A 629 TRP 0.034 0.001 TRP D 789 HIS 0.006 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00339 (18516) covalent geometry : angle 0.56622 (25020) SS BOND : bond 0.00243 ( 11) SS BOND : angle 0.80031 ( 22) hydrogen bonds : bond 0.03558 ( 1043) hydrogen bonds : angle 4.39414 ( 3027) Misc. bond : bond 0.00073 ( 1) *********************** 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 387 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 ASP cc_start: 0.9242 (m-30) cc_final: 0.8757 (p0) REVERT: A 518 MET cc_start: 0.8757 (ttt) cc_final: 0.8383 (tpp) REVERT: A 525 MET cc_start: 0.8787 (ttp) cc_final: 0.8292 (tmm) REVERT: A 531 LYS cc_start: 0.6600 (tptp) cc_final: 0.4924 (pptt) REVERT: A 538 SER cc_start: 0.8922 (p) cc_final: 0.7923 (m) REVERT: A 541 ASP cc_start: 0.9005 (m-30) cc_final: 0.8729 (m-30) REVERT: A 593 PHE cc_start: 0.2801 (m-80) cc_final: 0.2231 (m-80) REVERT: A 673 ASP cc_start: 0.9117 (t0) cc_final: 0.8791 (p0) REVERT: A 681 PHE cc_start: 0.9372 (m-80) cc_final: 0.9026 (m-80) REVERT: A 696 MET cc_start: 0.9092 (mmp) cc_final: 0.8791 (mmm) REVERT: B 433 ASN cc_start: 0.8673 (t0) cc_final: 0.8381 (t0) REVERT: B 525 MET cc_start: 0.8930 (ttm) cc_final: 0.8564 (tmm) REVERT: B 541 ASP cc_start: 0.8846 (m-30) cc_final: 0.8556 (t70) REVERT: B 683 ARG cc_start: 0.8902 (mtt-85) cc_final: 0.8625 (ttp-110) REVERT: B 692 MET cc_start: 0.9303 (mmt) cc_final: 0.9018 (mmm) REVERT: B 733 TYR cc_start: 0.8613 (t80) cc_final: 0.8129 (t80) REVERT: B 819 TYR cc_start: 0.9224 (m-10) cc_final: 0.8858 (m-80) REVERT: C 440 ASN cc_start: 0.8501 (m-40) cc_final: 0.8280 (m-40) REVERT: C 518 MET cc_start: 0.9099 (ttm) cc_final: 0.8421 (mtp) REVERT: C 525 MET cc_start: 0.8956 (ttm) cc_final: 0.7925 (tmm) REVERT: C 613 ILE cc_start: 0.8931 (tt) cc_final: 0.8600 (tp) REVERT: C 641 ASN cc_start: 0.9070 (t0) cc_final: 0.8853 (t0) REVERT: C 730 MET cc_start: 0.9296 (mpp) cc_final: 0.9001 (mpp) REVERT: D 525 MET cc_start: 0.8593 (ttm) cc_final: 0.8315 (tmm) REVERT: D 549 MET cc_start: 0.8322 (tpt) cc_final: 0.7781 (tpp) REVERT: D 551 ILE cc_start: 0.9390 (mm) cc_final: 0.9128 (mm) REVERT: D 748 ASN cc_start: 0.9361 (m-40) cc_final: 0.8997 (t0) REVERT: D 769 ASN cc_start: 0.9487 (t0) cc_final: 0.9211 (t0) REVERT: H 200 MET cc_start: 0.8947 (tpp) cc_final: 0.8737 (tmm) REVERT: F 96 TYR cc_start: 0.8487 (t80) cc_final: 0.8193 (t80) REVERT: F 117 MET cc_start: 0.9143 (mmm) cc_final: 0.8841 (mmm) REVERT: G 31 ASP cc_start: 0.8339 (p0) cc_final: 0.7731 (p0) REVERT: G 33 TRP cc_start: 0.9318 (m100) cc_final: 0.8942 (m100) REVERT: E 149 ASN cc_start: 0.9334 (t0) cc_final: 0.9106 (t0) REVERT: E 203 ASP cc_start: 0.9159 (t0) cc_final: 0.8849 (t0) REVERT: E 205 HIS cc_start: 0.8487 (t70) cc_final: 0.8276 (t70) outliers start: 1 outliers final: 0 residues processed: 386 average time/residue: 0.1124 time to fit residues: 68.8412 Evaluate side-chains 290 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 109 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 204 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN H 149 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.074382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.057873 restraints weight = 88652.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059483 restraints weight = 52946.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060621 restraints weight = 37057.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061360 restraints weight = 28634.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.061921 restraints weight = 24024.939| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18528 Z= 0.183 Angle : 0.591 9.604 25042 Z= 0.312 Chirality : 0.042 0.206 2800 Planarity : 0.004 0.050 3056 Dihedral : 6.936 105.630 2596 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.10 % Allowed : 1.77 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % 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: 1.77 (0.15), residues: 1302 sheet: -1.46 (0.43), residues: 130 loop : -1.08 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 650 TYR 0.022 0.001 TYR A 838 PHE 0.030 0.002 PHE H 182 TRP 0.033 0.002 TRP D 482 HIS 0.005 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00398 (18516) covalent geometry : angle 0.59086 (25020) SS BOND : bond 0.00262 ( 11) SS BOND : angle 0.79015 ( 22) hydrogen bonds : bond 0.03670 ( 1043) hydrogen bonds : angle 4.43108 ( 3027) Misc. bond : bond 0.00067 ( 1) *********************** 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 377 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 ASP cc_start: 0.9255 (m-30) cc_final: 0.8763 (p0) REVERT: A 518 MET cc_start: 0.8793 (ttt) cc_final: 0.8384 (tpp) REVERT: A 525 MET cc_start: 0.8716 (ttp) cc_final: 0.8285 (tmm) REVERT: A 541 ASP cc_start: 0.8992 (m-30) cc_final: 0.8791 (m-30) REVERT: A 593 PHE cc_start: 0.2722 (m-80) cc_final: 0.2133 (m-80) REVERT: A 673 ASP cc_start: 0.9123 (t0) cc_final: 0.8789 (p0) REVERT: A 681 PHE cc_start: 0.9385 (m-80) cc_final: 0.8957 (m-80) REVERT: A 692 MET cc_start: 0.9214 (mpp) cc_final: 0.8691 (mpp) REVERT: A 696 MET cc_start: 0.9036 (mmp) cc_final: 0.8745 (mmm) REVERT: A 743 MET cc_start: 0.8375 (pmm) cc_final: 0.7832 (pmm) REVERT: B 433 ASN cc_start: 0.8681 (t0) cc_final: 0.8401 (t0) REVERT: B 525 MET cc_start: 0.8956 (ttm) cc_final: 0.8609 (tmm) REVERT: B 541 ASP cc_start: 0.8846 (m-30) cc_final: 0.8562 (t70) REVERT: B 637 SER cc_start: 0.9799 (m) cc_final: 0.9547 (p) REVERT: B 683 ARG cc_start: 0.8910 (mtt-85) cc_final: 0.8667 (ttp-110) REVERT: B 692 MET cc_start: 0.9305 (mmt) cc_final: 0.9028 (mmm) REVERT: B 733 TYR cc_start: 0.8558 (t80) cc_final: 0.8210 (t80) REVERT: B 790 TYR cc_start: 0.8959 (m-80) cc_final: 0.8599 (m-80) REVERT: B 819 TYR cc_start: 0.9209 (m-10) cc_final: 0.8797 (m-80) REVERT: C 429 MET cc_start: 0.8351 (mpp) cc_final: 0.7990 (mpp) REVERT: C 440 ASN cc_start: 0.8558 (m-40) cc_final: 0.8229 (m110) REVERT: C 518 MET cc_start: 0.9155 (ttm) cc_final: 0.8532 (mtp) REVERT: C 525 MET cc_start: 0.9016 (ttm) cc_final: 0.7939 (tmm) REVERT: C 613 ILE cc_start: 0.8928 (tt) cc_final: 0.8630 (tp) REVERT: C 641 ASN cc_start: 0.9141 (t0) cc_final: 0.8934 (t0) REVERT: C 730 MET cc_start: 0.9191 (mpp) cc_final: 0.8958 (mpp) REVERT: D 525 MET cc_start: 0.8585 (ttm) cc_final: 0.8319 (tmm) REVERT: D 551 ILE cc_start: 0.9419 (mm) cc_final: 0.9145 (mm) REVERT: D 748 ASN cc_start: 0.9296 (m-40) cc_final: 0.8941 (m-40) REVERT: D 769 ASN cc_start: 0.9499 (t0) cc_final: 0.9255 (t0) REVERT: F 96 TYR cc_start: 0.8505 (t80) cc_final: 0.8228 (t80) REVERT: F 117 MET cc_start: 0.9141 (mmm) cc_final: 0.8858 (mmm) REVERT: F 200 MET cc_start: 0.9143 (ttm) cc_final: 0.8861 (mtt) REVERT: G 10 MET cc_start: 0.8585 (mpp) cc_final: 0.8339 (mpp) REVERT: G 31 ASP cc_start: 0.8442 (p0) cc_final: 0.7489 (p0) REVERT: G 33 TRP cc_start: 0.9335 (m100) cc_final: 0.8986 (m100) REVERT: G 206 LYS cc_start: 0.8673 (tptp) cc_final: 0.8452 (tppt) REVERT: E 203 ASP cc_start: 0.9174 (t0) cc_final: 0.8661 (t0) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.1096 time to fit residues: 65.8506 Evaluate side-chains 277 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.075054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058553 restraints weight = 87897.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060146 restraints weight = 52179.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061253 restraints weight = 36538.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.062037 restraints weight = 28513.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062572 restraints weight = 23845.013| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18528 Z= 0.149 Angle : 0.574 6.878 25042 Z= 0.302 Chirality : 0.042 0.214 2800 Planarity : 0.004 0.044 3056 Dihedral : 6.841 104.445 2596 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % 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: 0.91 (0.18), residues: 2256 helix: 1.80 (0.15), residues: 1302 sheet: -1.04 (0.45), residues: 120 loop : -1.10 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 737 TYR 0.023 0.001 TYR A 838 PHE 0.032 0.001 PHE A 629 TRP 0.048 0.002 TRP D 482 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00328 (18516) covalent geometry : angle 0.57368 (25020) SS BOND : bond 0.00225 ( 11) SS BOND : angle 0.75449 ( 22) hydrogen bonds : bond 0.03563 ( 1043) hydrogen bonds : angle 4.35337 ( 3027) Misc. bond : bond 0.00073 ( 1) *********************** 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 386 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 ASP cc_start: 0.9218 (m-30) cc_final: 0.8754 (p0) REVERT: A 525 MET cc_start: 0.8750 (ttp) cc_final: 0.8096 (tmm) REVERT: A 538 SER cc_start: 0.8944 (p) cc_final: 0.8035 (m) REVERT: A 541 ASP cc_start: 0.8957 (m-30) cc_final: 0.8729 (m-30) REVERT: A 593 PHE cc_start: 0.2644 (m-80) cc_final: 0.2087 (m-80) REVERT: A 608 GLN cc_start: 0.9309 (mp10) cc_final: 0.9060 (mp10) REVERT: A 673 ASP cc_start: 0.9063 (t0) cc_final: 0.8763 (p0) REVERT: A 681 PHE cc_start: 0.9318 (m-80) cc_final: 0.9087 (m-80) REVERT: A 743 MET cc_start: 0.8413 (pmm) cc_final: 0.7941 (pmm) REVERT: B 433 ASN cc_start: 0.8702 (t0) cc_final: 0.8378 (t0) REVERT: B 525 MET cc_start: 0.8907 (ttm) cc_final: 0.8546 (tmm) REVERT: B 541 ASP cc_start: 0.8807 (m-30) cc_final: 0.8559 (t70) REVERT: B 637 SER cc_start: 0.9778 (m) cc_final: 0.9520 (p) REVERT: B 683 ARG cc_start: 0.8866 (mtt-85) cc_final: 0.8650 (ttp-110) REVERT: B 692 MET cc_start: 0.9278 (mmt) cc_final: 0.9011 (mmm) REVERT: B 733 TYR cc_start: 0.8525 (t80) cc_final: 0.8169 (t80) REVERT: B 736 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8123 (tp-100) REVERT: B 790 TYR cc_start: 0.8911 (m-80) cc_final: 0.8499 (m-80) REVERT: B 819 TYR cc_start: 0.9157 (m-10) cc_final: 0.8725 (m-80) REVERT: C 429 MET cc_start: 0.8199 (mpp) cc_final: 0.7865 (mpp) REVERT: C 440 ASN cc_start: 0.8454 (m-40) cc_final: 0.8130 (m-40) REVERT: C 518 MET cc_start: 0.9085 (ttm) cc_final: 0.8461 (mtp) REVERT: C 525 MET cc_start: 0.8963 (ttm) cc_final: 0.7910 (tmm) REVERT: C 526 ILE cc_start: 0.9248 (tp) cc_final: 0.9025 (tp) REVERT: C 607 MET cc_start: 0.9068 (mmp) cc_final: 0.8801 (mmt) REVERT: C 613 ILE cc_start: 0.8956 (tt) cc_final: 0.8692 (tp) REVERT: C 730 MET cc_start: 0.9201 (mpp) cc_final: 0.8894 (mpp) REVERT: D 429 MET cc_start: 0.8611 (mpp) cc_final: 0.8379 (mpp) REVERT: D 485 MET cc_start: 0.8356 (mpp) cc_final: 0.8060 (mpp) REVERT: D 748 ASN cc_start: 0.9339 (m-40) cc_final: 0.9005 (t0) REVERT: D 769 ASN cc_start: 0.9489 (t0) cc_final: 0.9223 (t0) REVERT: F 96 TYR cc_start: 0.8432 (t80) cc_final: 0.8129 (t80) REVERT: F 117 MET cc_start: 0.9105 (mmm) cc_final: 0.8831 (mmm) REVERT: F 200 MET cc_start: 0.9128 (ttm) cc_final: 0.8841 (mtt) REVERT: G 10 MET cc_start: 0.8535 (mpp) cc_final: 0.8243 (mpp) REVERT: G 31 ASP cc_start: 0.8215 (p0) cc_final: 0.7675 (p0) REVERT: G 33 TRP cc_start: 0.9287 (m100) cc_final: 0.8863 (m100) REVERT: G 114 LEU cc_start: 0.9649 (mt) cc_final: 0.9425 (mt) REVERT: E 203 ASP cc_start: 0.9060 (t0) cc_final: 0.8732 (t0) REVERT: E 205 HIS cc_start: 0.8427 (t70) cc_final: 0.8218 (t70) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.1056 time to fit residues: 64.6258 Evaluate side-chains 296 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** E 60 HIS ** 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 = 0.3594 r_free = 0.3594 target = 0.076363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059764 restraints weight = 86890.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061393 restraints weight = 51550.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062518 restraints weight = 36241.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063316 restraints weight = 28266.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063838 restraints weight = 23663.171| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18528 Z= 0.126 Angle : 0.578 8.225 25042 Z= 0.301 Chirality : 0.042 0.223 2800 Planarity : 0.004 0.046 3056 Dihedral : 6.747 104.123 2596 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % 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: 0.92 (0.18), residues: 2256 helix: 1.85 (0.15), residues: 1291 sheet: -1.13 (0.43), residues: 125 loop : -1.11 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 683 TYR 0.025 0.001 TYR D 545 PHE 0.022 0.001 PHE H 182 TRP 0.048 0.002 TRP D 482 HIS 0.006 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00282 (18516) covalent geometry : angle 0.57776 (25020) SS BOND : bond 0.00186 ( 11) SS BOND : angle 0.72764 ( 22) hydrogen bonds : bond 0.03475 ( 1043) hydrogen bonds : angle 4.35184 ( 3027) Misc. bond : bond 0.00077 ( 1) *********************** 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 393 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.640 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 429 MET cc_start: 0.9101 (mpp) cc_final: 0.8746 (mpp) REVERT: A 478 ASP cc_start: 0.9200 (m-30) cc_final: 0.8701 (p0) REVERT: A 525 MET cc_start: 0.8680 (ttp) cc_final: 0.8119 (tmm) REVERT: A 538 SER cc_start: 0.8965 (p) cc_final: 0.8046 (m) REVERT: A 541 ASP cc_start: 0.8966 (m-30) cc_final: 0.8732 (m-30) REVERT: A 593 PHE cc_start: 0.2602 (m-80) cc_final: 0.2058 (m-80) REVERT: A 630 PHE cc_start: 0.9486 (t80) cc_final: 0.9241 (t80) REVERT: A 673 ASP cc_start: 0.8999 (t0) cc_final: 0.8790 (p0) REVERT: A 681 PHE cc_start: 0.9293 (m-80) cc_final: 0.9007 (m-80) REVERT: A 743 MET cc_start: 0.8355 (pmm) cc_final: 0.7934 (pmm) REVERT: B 423 MET cc_start: 0.8253 (tpt) cc_final: 0.6228 (tpt) REVERT: B 433 ASN cc_start: 0.8731 (t0) cc_final: 0.8417 (t0) REVERT: B 525 MET cc_start: 0.8834 (ttm) cc_final: 0.8518 (tmm) REVERT: B 541 ASP cc_start: 0.8782 (m-30) cc_final: 0.8545 (t70) REVERT: B 630 PHE cc_start: 0.9281 (t80) cc_final: 0.9080 (t80) REVERT: B 637 SER cc_start: 0.9775 (m) cc_final: 0.9520 (p) REVERT: B 683 ARG cc_start: 0.8866 (mtt-85) cc_final: 0.8648 (ttp-110) REVERT: B 692 MET cc_start: 0.9293 (mmt) cc_final: 0.9036 (mmm) REVERT: B 733 TYR cc_start: 0.8487 (t80) cc_final: 0.8217 (t80) REVERT: B 736 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8191 (tp-100) REVERT: B 819 TYR cc_start: 0.9139 (m-10) cc_final: 0.8744 (m-80) REVERT: C 429 MET cc_start: 0.8199 (mpp) cc_final: 0.7868 (mpp) REVERT: C 440 ASN cc_start: 0.8426 (m-40) cc_final: 0.8155 (m-40) REVERT: C 485 MET cc_start: 0.8841 (ptp) cc_final: 0.8559 (pmm) REVERT: C 518 MET cc_start: 0.9055 (ttm) cc_final: 0.8339 (mtm) REVERT: C 525 MET cc_start: 0.8984 (ttm) cc_final: 0.7920 (tmm) REVERT: C 526 ILE cc_start: 0.9239 (tp) cc_final: 0.9035 (tp) REVERT: C 553 PHE cc_start: 0.8964 (m-80) cc_final: 0.8480 (m-80) REVERT: C 607 MET cc_start: 0.9047 (mmp) cc_final: 0.8644 (mmt) REVERT: C 613 ILE cc_start: 0.8938 (tt) cc_final: 0.8684 (tp) REVERT: C 730 MET cc_start: 0.9201 (mpp) cc_final: 0.8871 (mpp) REVERT: D 485 MET cc_start: 0.8287 (mpp) cc_final: 0.7976 (mpp) REVERT: D 525 MET cc_start: 0.8318 (tmm) cc_final: 0.8068 (tmm) REVERT: D 748 ASN cc_start: 0.9570 (m-40) cc_final: 0.9066 (t0) REVERT: D 769 ASN cc_start: 0.9503 (t0) cc_final: 0.9234 (t0) REVERT: H 58 MET cc_start: 0.8523 (tpp) cc_final: 0.7631 (tpp) REVERT: F 117 MET cc_start: 0.9048 (mmm) cc_final: 0.8833 (mmp) REVERT: F 200 MET cc_start: 0.9086 (ttm) cc_final: 0.8781 (mtt) REVERT: G 31 ASP cc_start: 0.8194 (p0) cc_final: 0.7714 (p0) REVERT: G 33 TRP cc_start: 0.9241 (m100) cc_final: 0.8746 (m100) REVERT: G 114 LEU cc_start: 0.9631 (mt) cc_final: 0.9420 (mt) REVERT: E 142 PHE cc_start: 0.9336 (m-80) cc_final: 0.8808 (m-80) REVERT: E 203 ASP cc_start: 0.9058 (t0) cc_final: 0.8747 (t0) REVERT: E 205 HIS cc_start: 0.8384 (t70) cc_final: 0.8181 (t70) outliers start: 1 outliers final: 0 residues processed: 392 average time/residue: 0.1082 time to fit residues: 67.5835 Evaluate side-chains 298 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.075996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059491 restraints weight = 87811.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.061120 restraints weight = 52847.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062252 restraints weight = 37141.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063053 restraints weight = 28843.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.063524 restraints weight = 24024.299| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18528 Z= 0.142 Angle : 0.596 7.702 25042 Z= 0.311 Chirality : 0.042 0.197 2800 Planarity : 0.004 0.048 3056 Dihedral : 6.732 102.258 2596 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2256 helix: 1.88 (0.15), residues: 1278 sheet: -1.37 (0.42), residues: 132 loop : -0.97 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 683 TYR 0.024 0.001 TYR D 545 PHE 0.036 0.001 PHE A 629 TRP 0.032 0.001 TRP D 482 HIS 0.006 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00317 (18516) covalent geometry : angle 0.59562 (25020) SS BOND : bond 0.00210 ( 11) SS BOND : angle 0.74551 ( 22) hydrogen bonds : bond 0.03567 ( 1043) hydrogen bonds : angle 4.42533 ( 3027) Misc. bond : bond 0.00065 ( 1) *********************** 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 387 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 ASP cc_start: 0.9219 (m-30) cc_final: 0.8775 (p0) REVERT: A 525 MET cc_start: 0.8710 (ttp) cc_final: 0.8137 (tmm) REVERT: A 538 SER cc_start: 0.9008 (p) cc_final: 0.8111 (m) REVERT: A 541 ASP cc_start: 0.9011 (m-30) cc_final: 0.8768 (m-30) REVERT: A 593 PHE cc_start: 0.2517 (m-80) cc_final: 0.1994 (m-80) REVERT: A 673 ASP cc_start: 0.9003 (t0) cc_final: 0.8799 (p0) REVERT: A 681 PHE cc_start: 0.9339 (m-80) cc_final: 0.9027 (m-80) REVERT: A 743 MET cc_start: 0.8265 (pmm) cc_final: 0.7616 (pmm) REVERT: B 423 MET cc_start: 0.7138 (tpt) cc_final: 0.6517 (tpt) REVERT: B 433 ASN cc_start: 0.8742 (t0) cc_final: 0.8398 (t0) REVERT: B 525 MET cc_start: 0.8786 (ttm) cc_final: 0.8565 (tmm) REVERT: B 541 ASP cc_start: 0.8781 (m-30) cc_final: 0.8556 (t70) REVERT: B 637 SER cc_start: 0.9795 (m) cc_final: 0.9548 (p) REVERT: B 683 ARG cc_start: 0.8919 (mtt-85) cc_final: 0.8685 (ttp-110) REVERT: B 733 TYR cc_start: 0.8600 (t80) cc_final: 0.8268 (t80) REVERT: B 736 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8211 (tp-100) REVERT: B 790 TYR cc_start: 0.8878 (m-80) cc_final: 0.8453 (m-80) REVERT: B 810 SER cc_start: 0.8784 (p) cc_final: 0.8519 (p) REVERT: B 819 TYR cc_start: 0.9197 (m-10) cc_final: 0.8749 (m-80) REVERT: C 429 MET cc_start: 0.8384 (mpp) cc_final: 0.8075 (mpp) REVERT: C 440 ASN cc_start: 0.8466 (m-40) cc_final: 0.8195 (m-40) REVERT: C 518 MET cc_start: 0.9079 (ttm) cc_final: 0.8366 (mtm) REVERT: C 525 MET cc_start: 0.9037 (ttm) cc_final: 0.7938 (tmm) REVERT: C 526 ILE cc_start: 0.9279 (tp) cc_final: 0.9070 (tp) REVERT: C 553 PHE cc_start: 0.9011 (m-80) cc_final: 0.8536 (m-80) REVERT: C 613 ILE cc_start: 0.8948 (tt) cc_final: 0.8689 (tp) REVERT: C 730 MET cc_start: 0.9236 (mpp) cc_final: 0.8914 (mpp) REVERT: D 485 MET cc_start: 0.8290 (mpp) cc_final: 0.8016 (mpp) REVERT: D 525 MET cc_start: 0.8438 (tmm) cc_final: 0.8108 (tmm) REVERT: D 551 ILE cc_start: 0.9443 (mm) cc_final: 0.9179 (mm) REVERT: D 748 ASN cc_start: 0.9508 (m-40) cc_final: 0.8912 (t0) REVERT: D 769 ASN cc_start: 0.9532 (t0) cc_final: 0.9264 (t0) REVERT: H 58 MET cc_start: 0.8487 (tpp) cc_final: 0.7713 (tpp) REVERT: F 117 MET cc_start: 0.9094 (mmm) cc_final: 0.8823 (mmm) REVERT: F 200 MET cc_start: 0.9107 (ttm) cc_final: 0.8844 (mtt) REVERT: G 31 ASP cc_start: 0.8248 (p0) cc_final: 0.7741 (p0) REVERT: G 33 TRP cc_start: 0.9285 (m100) cc_final: 0.8907 (m100) REVERT: G 114 LEU cc_start: 0.9638 (mt) cc_final: 0.9428 (mt) REVERT: E 142 PHE cc_start: 0.9320 (m-80) cc_final: 0.8857 (m-80) REVERT: E 203 ASP cc_start: 0.9112 (t0) cc_final: 0.8810 (t0) REVERT: E 205 HIS cc_start: 0.8398 (t70) cc_final: 0.8187 (t70) outliers start: 1 outliers final: 0 residues processed: 386 average time/residue: 0.1112 time to fit residues: 68.9123 Evaluate side-chains 302 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 213 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 135 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN B 609 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.3610 r_free = 0.3610 target = 0.077193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060768 restraints weight = 87107.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.062428 restraints weight = 52541.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063574 restraints weight = 36785.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064382 restraints weight = 28497.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.064987 restraints weight = 23763.980| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18528 Z= 0.120 Angle : 0.598 8.627 25042 Z= 0.309 Chirality : 0.042 0.286 2800 Planarity : 0.003 0.045 3056 Dihedral : 6.618 101.398 2596 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.05 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % 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: 1.78 (0.15), residues: 1288 sheet: -1.36 (0.42), residues: 135 loop : -1.07 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 65 TYR 0.026 0.001 TYR D 545 PHE 0.035 0.001 PHE A 630 TRP 0.035 0.002 TRP D 789 HIS 0.007 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00269 (18516) covalent geometry : angle 0.59822 (25020) SS BOND : bond 0.00166 ( 11) SS BOND : angle 0.71828 ( 22) hydrogen bonds : bond 0.03510 ( 1043) hydrogen bonds : angle 4.37306 ( 3027) Misc. bond : bond 0.00081 ( 1) ********************** 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 389 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8499 (mmm) cc_final: 0.8268 (tpt) REVERT: A 429 MET cc_start: 0.9094 (mpp) cc_final: 0.8736 (mpp) REVERT: A 478 ASP cc_start: 0.9195 (m-30) cc_final: 0.8708 (p0) REVERT: A 525 MET cc_start: 0.8677 (ttp) cc_final: 0.8278 (tmm) REVERT: A 538 SER cc_start: 0.9019 (p) cc_final: 0.8099 (m) REVERT: A 541 ASP cc_start: 0.9015 (m-30) cc_final: 0.8772 (m-30) REVERT: A 593 PHE cc_start: 0.2508 (m-80) cc_final: 0.1978 (m-80) REVERT: A 607 MET cc_start: 0.9158 (mmm) cc_final: 0.8606 (mmm) REVERT: A 681 PHE cc_start: 0.9316 (m-80) cc_final: 0.9020 (m-80) REVERT: A 743 MET cc_start: 0.8198 (pmm) cc_final: 0.7594 (pmm) REVERT: B 433 ASN cc_start: 0.8769 (t0) cc_final: 0.8545 (t0) REVERT: B 541 ASP cc_start: 0.8768 (m-30) cc_final: 0.8535 (t0) REVERT: B 683 ARG cc_start: 0.8918 (mtt-85) cc_final: 0.8678 (ttp-110) REVERT: B 733 TYR cc_start: 0.8533 (t80) cc_final: 0.8193 (t80) REVERT: B 736 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8174 (tp-100) REVERT: B 810 SER cc_start: 0.8769 (p) cc_final: 0.8360 (p) REVERT: B 819 TYR cc_start: 0.9160 (m-10) cc_final: 0.8777 (m-80) REVERT: C 429 MET cc_start: 0.8318 (mpp) cc_final: 0.8049 (mpp) REVERT: C 488 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8896 (mt-10) REVERT: C 518 MET cc_start: 0.9071 (ttm) cc_final: 0.8347 (mtm) REVERT: C 525 MET cc_start: 0.9041 (ttm) cc_final: 0.7938 (tmm) REVERT: C 553 PHE cc_start: 0.8947 (m-80) cc_final: 0.8454 (m-80) REVERT: C 603 LEU cc_start: 0.9249 (tp) cc_final: 0.9043 (tp) REVERT: C 613 ILE cc_start: 0.8938 (tt) cc_final: 0.8687 (tp) REVERT: C 690 GLU cc_start: 0.9444 (tp30) cc_final: 0.9177 (mm-30) REVERT: C 730 MET cc_start: 0.9229 (mpp) cc_final: 0.8858 (mpp) REVERT: D 485 MET cc_start: 0.8269 (mpp) cc_final: 0.7692 (mpp) REVERT: D 525 MET cc_start: 0.8448 (tmm) cc_final: 0.8132 (tmm) REVERT: D 551 ILE cc_start: 0.9439 (mm) cc_final: 0.9172 (mm) REVERT: D 748 ASN cc_start: 0.9559 (m-40) cc_final: 0.8919 (t0) REVERT: D 769 ASN cc_start: 0.9559 (t0) cc_final: 0.9241 (t0) REVERT: F 106 ILE cc_start: 0.8871 (tp) cc_final: 0.8642 (tp) REVERT: F 117 MET cc_start: 0.8985 (mmm) cc_final: 0.8774 (mmm) REVERT: F 200 MET cc_start: 0.9101 (ttm) cc_final: 0.8796 (mtt) REVERT: G 31 ASP cc_start: 0.8172 (p0) cc_final: 0.7691 (p0) REVERT: G 33 TRP cc_start: 0.9236 (m100) cc_final: 0.8738 (m100) REVERT: G 114 LEU cc_start: 0.9517 (mt) cc_final: 0.9150 (mt) REVERT: G 117 MET cc_start: 0.9089 (mpp) cc_final: 0.8889 (mpp) REVERT: E 142 PHE cc_start: 0.9271 (m-80) cc_final: 0.8918 (m-80) REVERT: E 203 ASP cc_start: 0.8974 (t0) cc_final: 0.8612 (t0) outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.1045 time to fit residues: 65.2279 Evaluate side-chains 301 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 213 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN C 641 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN E 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.077792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.060867 restraints weight = 87735.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.062594 restraints weight = 52258.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.063764 restraints weight = 36234.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064606 restraints weight = 28091.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065002 restraints weight = 23356.819| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18528 Z= 0.123 Angle : 0.609 8.244 25042 Z= 0.316 Chirality : 0.042 0.211 2800 Planarity : 0.003 0.046 3056 Dihedral : 6.605 101.390 2596 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.05 % Allowed : 0.31 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.05 % 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: 0.86 (0.18), residues: 2256 helix: 1.75 (0.15), residues: 1283 sheet: -1.43 (0.44), residues: 115 loop : -0.98 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 683 TYR 0.026 0.001 TYR D 545 PHE 0.034 0.001 PHE A 629 TRP 0.021 0.001 TRP D 482 HIS 0.007 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00278 (18516) covalent geometry : angle 0.60918 (25020) SS BOND : bond 0.00178 ( 11) SS BOND : angle 0.73510 ( 22) hydrogen bonds : bond 0.03499 ( 1043) hydrogen bonds : angle 4.42590 ( 3027) Misc. bond : bond 0.00077 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.67 seconds wall clock time: 52 minutes 2.89 seconds (3122.89 seconds total)