Starting phenix.real_space_refine on Sun Aug 24 20:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bpq_7127/08_2025/6bpq_7127_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bpq_7127/08_2025/6bpq_7127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bpq_7127/08_2025/6bpq_7127_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bpq_7127/08_2025/6bpq_7127_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bpq_7127/08_2025/6bpq_7127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bpq_7127/08_2025/6bpq_7127.map" } resolution = 4.1 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= 0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 14624 2.51 5 N 3808 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22404 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 690 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'UNK:plan-1': 20, 'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 4544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4544 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 17, 'TRANS': 645} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 934 Unresolved non-hydrogen angles: 1171 Unresolved non-hydrogen dihedrals: 743 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'UNK:plan-1': 5, 'ARG:plan': 19, 'ASP:plan': 21, 'TYR:plan': 5, 'ASN:plan1': 18, 'GLU:plan': 38, 'GLN:plan1': 15, 'PHE:plan': 7, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 528 Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 247 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 18, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Restraints were copied for chains: B, C, D Time building chain proxies: 5.16, per 1000 atoms: 0.23 Number of scatterers: 22404 At special positions: 0 Unit cell: (145.41, 145.41, 140.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3900 8.00 N 3808 7.00 C 14624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK A1010 " - " THR A1009 " " UNK B1010 " - " THR B1009 " " UNK C1010 " - " THR C1009 " " UNK D1010 " - " THR D1009 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 12 sheets defined 82.6% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.641A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.729A pdb=" N TYR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.788A pdb=" N TYR A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 296 " --> pdb=" O SER A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 385 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.835A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.578A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 481 removed outlier: 4.334A pdb=" N LEU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.548A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 4.095A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 607 through 636 removed outlier: 4.485A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 removed outlier: 4.102A pdb=" N THR A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 701 through 710 removed outlier: 6.037A pdb=" N CYS A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLY A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 765 through 789 Processing helix chain 'A' and resid 796 through 815 removed outlier: 3.779A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 851 Processing helix chain 'A' and resid 854 through 889 removed outlier: 4.256A pdb=" N MET A 858 " --> pdb=" O PRO A 854 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 910 Proline residue: A 906 - end of helix Processing helix chain 'A' and resid 949 through 953 removed outlier: 3.599A pdb=" N GLU A 952 " --> pdb=" O ARG A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 974 removed outlier: 3.540A pdb=" N LEU A 964 " --> pdb=" O CYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1008 Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1025 Processing helix chain 'A' and resid 1046 through 1067 removed outlier: 3.667A pdb=" N GLU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1100 Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.641A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.729A pdb=" N TYR B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.788A pdb=" N TYR B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 296 " --> pdb=" O SER B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 296' Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 385 Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.835A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.578A pdb=" N THR B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 481 removed outlier: 4.334A pdb=" N LEU B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.548A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 removed outlier: 4.095A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 607 through 636 removed outlier: 4.485A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 4.102A pdb=" N THR B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 701 through 710 removed outlier: 6.037A pdb=" N CYS B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 731 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 789 Processing helix chain 'B' and resid 796 through 815 removed outlier: 3.779A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 803 " --> pdb=" O ASN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 851 Processing helix chain 'B' and resid 854 through 889 removed outlier: 4.255A pdb=" N MET B 858 " --> pdb=" O PRO B 854 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 910 Proline residue: B 906 - end of helix Processing helix chain 'B' and resid 949 through 953 removed outlier: 3.598A pdb=" N GLU B 952 " --> pdb=" O ARG B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 974 removed outlier: 3.540A pdb=" N LEU B 964 " --> pdb=" O CYS B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1008 Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1025 Processing helix chain 'B' and resid 1046 through 1067 removed outlier: 3.666A pdb=" N GLU B1050 " --> pdb=" O ASN B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1100 Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.640A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.729A pdb=" N TYR C 251 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.787A pdb=" N TYR C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY C 296 " --> pdb=" O SER C 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 296' Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 385 Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.834A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.578A pdb=" N THR C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 481 removed outlier: 4.334A pdb=" N LEU C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.547A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 566 " --> pdb=" O GLN C 562 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 583 removed outlier: 4.095A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 603 Processing helix chain 'C' and resid 607 through 636 removed outlier: 4.484A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 627 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 645 removed outlier: 4.102A pdb=" N THR C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 701 through 710 removed outlier: 6.038A pdb=" N CYS C 707 " --> pdb=" O PRO C 703 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLY C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 710 " --> pdb=" O GLY C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 731 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 789 Processing helix chain 'C' and resid 796 through 815 removed outlier: 3.780A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 803 " --> pdb=" O ASN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 851 Processing helix chain 'C' and resid 854 through 889 removed outlier: 4.255A pdb=" N MET C 858 " --> pdb=" O PRO C 854 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 889 " --> pdb=" O GLN C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 910 Proline residue: C 906 - end of helix Processing helix chain 'C' and resid 949 through 953 removed outlier: 3.599A pdb=" N GLU C 952 " --> pdb=" O ARG C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 974 removed outlier: 3.540A pdb=" N LEU C 964 " --> pdb=" O CYS C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1008 Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1025 Processing helix chain 'C' and resid 1046 through 1067 removed outlier: 3.667A pdb=" N GLU C1050 " --> pdb=" O ASN C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1100 Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.640A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.729A pdb=" N TYR D 251 " --> pdb=" O ARG D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.787A pdb=" N TYR D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY D 296 " --> pdb=" O SER D 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 292 through 296' Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 352 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 385 Processing helix chain 'D' and resid 403 through 420 Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.834A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.578A pdb=" N THR D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 481 removed outlier: 4.334A pdb=" N LEU D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.548A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 566 " --> pdb=" O GLN D 562 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP D 567 " --> pdb=" O ALA D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 583 removed outlier: 4.095A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 603 Processing helix chain 'D' and resid 607 through 636 removed outlier: 4.484A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 627 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 removed outlier: 4.102A pdb=" N THR D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 701 through 710 removed outlier: 6.038A pdb=" N CYS D 707 " --> pdb=" O PRO D 703 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLY D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 710 " --> pdb=" O GLY D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 731 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 765 through 789 Processing helix chain 'D' and resid 796 through 815 removed outlier: 3.780A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR D 803 " --> pdb=" O ASN D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 851 Processing helix chain 'D' and resid 854 through 889 removed outlier: 4.255A pdb=" N MET D 858 " --> pdb=" O PRO D 854 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG D 889 " --> pdb=" O GLN D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 910 Proline residue: D 906 - end of helix Processing helix chain 'D' and resid 949 through 953 removed outlier: 3.599A pdb=" N GLU D 952 " --> pdb=" O ARG D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 974 removed outlier: 3.540A pdb=" N LEU D 964 " --> pdb=" O CYS D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 1008 Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1025 Processing helix chain 'D' and resid 1046 through 1067 removed outlier: 3.667A pdb=" N GLU D1050 " --> pdb=" O ASN D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1100 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 removed outlier: 6.918A pdb=" N UNK A 106 " --> pdb=" O UNK A 116 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N UNK A 118 " --> pdb=" O UNK A 106 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N UNK A 108 " --> pdb=" O UNK A 118 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N UNK A 120 " --> pdb=" O UNK A 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N UNK A 117 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LEU A 262 " --> pdb=" O UNK A 117 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N UNK A 119 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.943A pdb=" N VAL A 145 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.041A pdb=" N VAL A 327 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE A 394 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 329 " --> pdb=" O ILE A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.918A pdb=" N UNK B 106 " --> pdb=" O UNK B 116 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N UNK B 118 " --> pdb=" O UNK B 106 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N UNK B 108 " --> pdb=" O UNK B 118 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N UNK B 120 " --> pdb=" O UNK B 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N UNK B 117 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU B 262 " --> pdb=" O UNK B 117 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N UNK B 119 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 212 removed outlier: 6.944A pdb=" N VAL B 145 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.041A pdb=" N VAL B 327 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE B 394 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 329 " --> pdb=" O ILE B 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 58 removed outlier: 6.918A pdb=" N UNK C 106 " --> pdb=" O UNK C 116 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N UNK C 118 " --> pdb=" O UNK C 106 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N UNK C 108 " --> pdb=" O UNK C 118 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N UNK C 120 " --> pdb=" O UNK C 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N UNK C 117 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU C 262 " --> pdb=" O UNK C 117 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N UNK C 119 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 210 through 212 removed outlier: 6.943A pdb=" N VAL C 145 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.040A pdb=" N VAL C 327 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE C 394 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 329 " --> pdb=" O ILE C 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 58 removed outlier: 6.918A pdb=" N UNK D 106 " --> pdb=" O UNK D 116 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N UNK D 118 " --> pdb=" O UNK D 106 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N UNK D 108 " --> pdb=" O UNK D 118 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N UNK D 120 " --> pdb=" O UNK D 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N UNK D 117 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU D 262 " --> pdb=" O UNK D 117 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N UNK D 119 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 210 through 212 removed outlier: 6.943A pdb=" N VAL D 145 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.040A pdb=" N VAL D 327 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE D 394 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 329 " --> pdb=" O ILE D 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1728 hydrogen bonds defined for protein. 5172 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: 4.49 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6949 1.34 - 1.46: 4544 1.46 - 1.57: 11267 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 22864 Sorted by residual: bond pdb=" C ASP C 248 " pdb=" N PRO C 249 " ideal model delta sigma weight residual 1.337 1.384 -0.047 1.24e-02 6.50e+03 1.41e+01 bond pdb=" C ASP D 248 " pdb=" N PRO D 249 " ideal model delta sigma weight residual 1.337 1.384 -0.047 1.24e-02 6.50e+03 1.41e+01 bond pdb=" C ASP A 248 " pdb=" N PRO A 249 " ideal model delta sigma weight residual 1.337 1.384 -0.047 1.24e-02 6.50e+03 1.41e+01 bond pdb=" C ASP B 248 " pdb=" N PRO B 249 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.24e-02 6.50e+03 1.39e+01 bond pdb=" CB TRP A 740 " pdb=" CG TRP A 740 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.81e+00 ... (remaining 22859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 30374 2.27 - 4.54: 858 4.54 - 6.82: 132 6.82 - 9.09: 20 9.09 - 11.36: 8 Bond angle restraints: 31392 Sorted by residual: angle pdb=" C LYS C 762 " pdb=" CA LYS C 762 " pdb=" CB LYS C 762 " ideal model delta sigma weight residual 116.63 110.74 5.89 1.16e+00 7.43e-01 2.58e+01 angle pdb=" C LYS D 762 " pdb=" CA LYS D 762 " pdb=" CB LYS D 762 " ideal model delta sigma weight residual 116.63 110.74 5.89 1.16e+00 7.43e-01 2.58e+01 angle pdb=" C LYS B 762 " pdb=" CA LYS B 762 " pdb=" CB LYS B 762 " ideal model delta sigma weight residual 116.63 110.76 5.87 1.16e+00 7.43e-01 2.57e+01 angle pdb=" C LYS A 762 " pdb=" CA LYS A 762 " pdb=" CB LYS A 762 " ideal model delta sigma weight residual 116.63 110.78 5.85 1.16e+00 7.43e-01 2.54e+01 angle pdb=" CA LYS A 762 " pdb=" C LYS A 762 " pdb=" N GLU A 763 " ideal model delta sigma weight residual 119.63 116.23 3.40 8.10e-01 1.52e+00 1.76e+01 ... (remaining 31387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 12325 15.56 - 31.13: 575 31.13 - 46.69: 68 46.69 - 62.25: 12 62.25 - 77.82: 12 Dihedral angle restraints: 12992 sinusoidal: 3180 harmonic: 9812 Sorted by residual: dihedral pdb=" CA ILE B 324 " pdb=" C ILE B 324 " pdb=" N PRO B 325 " pdb=" CA PRO B 325 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ILE D 324 " pdb=" C ILE D 324 " pdb=" N PRO D 325 " pdb=" CA PRO D 325 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ILE C 324 " pdb=" C ILE C 324 " pdb=" N PRO C 325 " pdb=" CA PRO C 325 " ideal model delta harmonic sigma weight residual 180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 12989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3149 0.065 - 0.129: 620 0.129 - 0.194: 87 0.194 - 0.258: 8 0.258 - 0.323: 4 Chirality restraints: 3868 Sorted by residual: chirality pdb=" CB ILE B 146 " pdb=" CA ILE B 146 " pdb=" CG1 ILE B 146 " pdb=" CG2 ILE B 146 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE C 146 " pdb=" CA ILE C 146 " pdb=" CG1 ILE C 146 " pdb=" CG2 ILE C 146 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE D 146 " pdb=" CA ILE D 146 " pdb=" CG1 ILE D 146 " pdb=" CG2 ILE D 146 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3865 not shown) Planarity restraints: 3944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 963 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C MET B 963 " -0.054 2.00e-02 2.50e+03 pdb=" O MET B 963 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 964 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 963 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C MET A 963 " -0.054 2.00e-02 2.50e+03 pdb=" O MET A 963 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 964 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 993 " 0.033 2.00e-02 2.50e+03 1.96e-02 9.60e+00 pdb=" CG TRP B 993 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 993 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 993 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP B 993 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP B 993 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 993 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 993 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 993 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 993 " -0.004 2.00e-02 2.50e+03 ... (remaining 3941 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8045 2.85 - 3.36: 22070 3.36 - 3.88: 35626 3.88 - 4.39: 36977 4.39 - 4.90: 61828 Nonbonded interactions: 164546 Sorted by model distance: nonbonded pdb=" O LEU D 592 " pdb=" OG SER D 595 " model vdw 2.338 3.040 nonbonded pdb=" O LEU B 592 " pdb=" OG SER B 595 " model vdw 2.338 3.040 nonbonded pdb=" O LEU C 592 " pdb=" OG SER C 595 " model vdw 2.338 3.040 nonbonded pdb=" O LEU A 592 " pdb=" OG SER A 595 " model vdw 2.338 3.040 nonbonded pdb=" O SER B 823 " pdb=" OG SER B 826 " model vdw 2.346 3.040 ... (remaining 164541 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.740 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.007 0.057 22868 Z= 0.313 Angle : 0.918 11.361 31404 Z= 0.503 Chirality : 0.053 0.323 3868 Planarity : 0.007 0.071 3940 Dihedral : 9.823 73.908 6524 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.12), residues: 2952 helix: -1.92 (0.08), residues: 2132 sheet: -3.19 (0.75), residues: 40 loop : -2.27 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 532 TYR 0.027 0.003 TYR A 772 PHE 0.043 0.003 PHE B 867 TRP 0.042 0.003 TRP B 993 HIS 0.009 0.003 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00662 (22864) covalent geometry : angle 0.91787 (31392) hydrogen bonds : bond 0.14059 ( 1728) hydrogen bonds : angle 6.52315 ( 5172) link_TRANS : bond 0.00223 ( 4) link_TRANS : angle 0.80445 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.886 Fit side-chains REVERT: A 525 TRP cc_start: 0.8213 (t60) cc_final: 0.7863 (t60) REVERT: A 615 GLU cc_start: 0.8276 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 752 PHE cc_start: 0.8588 (t80) cc_final: 0.8217 (t80) REVERT: A 772 TYR cc_start: 0.8277 (m-80) cc_final: 0.7795 (m-80) REVERT: A 835 TYR cc_start: 0.8906 (t80) cc_final: 0.8660 (t80) REVERT: B 170 TYR cc_start: 0.8387 (t80) cc_final: 0.8130 (t80) REVERT: B 525 TRP cc_start: 0.8233 (t60) cc_final: 0.7854 (t60) REVERT: B 615 GLU cc_start: 0.8230 (tt0) cc_final: 0.7970 (tm-30) REVERT: B 752 PHE cc_start: 0.8662 (t80) cc_final: 0.8196 (t80) REVERT: B 772 TYR cc_start: 0.8071 (m-80) cc_final: 0.7811 (m-80) REVERT: B 835 TYR cc_start: 0.8801 (t80) cc_final: 0.8542 (t80) REVERT: B 844 HIS cc_start: 0.9090 (t70) cc_final: 0.8844 (t-90) REVERT: C 170 TYR cc_start: 0.8388 (t80) cc_final: 0.8133 (t80) REVERT: C 525 TRP cc_start: 0.8234 (t60) cc_final: 0.7856 (t60) REVERT: C 615 GLU cc_start: 0.8233 (tt0) cc_final: 0.7991 (tm-30) REVERT: C 752 PHE cc_start: 0.8663 (t80) cc_final: 0.8196 (t80) REVERT: C 772 TYR cc_start: 0.8072 (m-80) cc_final: 0.7815 (m-80) REVERT: C 835 TYR cc_start: 0.8796 (t80) cc_final: 0.8535 (t80) REVERT: C 844 HIS cc_start: 0.9085 (t70) cc_final: 0.8848 (t-90) REVERT: D 170 TYR cc_start: 0.8388 (t80) cc_final: 0.8133 (t80) REVERT: D 525 TRP cc_start: 0.8234 (t60) cc_final: 0.7857 (t60) REVERT: D 615 GLU cc_start: 0.8231 (tt0) cc_final: 0.7989 (tm-30) REVERT: D 752 PHE cc_start: 0.8690 (t80) cc_final: 0.8243 (t80) REVERT: D 772 TYR cc_start: 0.8071 (m-80) cc_final: 0.7812 (m-80) REVERT: D 835 TYR cc_start: 0.8798 (t80) cc_final: 0.8538 (t80) REVERT: D 844 HIS cc_start: 0.9087 (t70) cc_final: 0.8852 (t-90) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1417 time to fit residues: 114.7780 Evaluate side-chains 255 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103759 restraints weight = 77173.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103820 restraints weight = 77765.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104613 restraints weight = 60312.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104823 restraints weight = 42790.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104947 restraints weight = 41855.397| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22868 Z= 0.234 Angle : 0.661 6.375 31404 Z= 0.354 Chirality : 0.042 0.158 3868 Planarity : 0.005 0.065 3940 Dihedral : 5.194 23.568 3412 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.15), residues: 2952 helix: 0.04 (0.10), residues: 2232 sheet: -3.58 (0.69), residues: 40 loop : -1.73 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 532 TYR 0.011 0.002 TYR D 907 PHE 0.017 0.002 PHE A 629 TRP 0.032 0.002 TRP B 993 HIS 0.007 0.002 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00510 (22864) covalent geometry : angle 0.66075 (31392) hydrogen bonds : bond 0.04211 ( 1728) hydrogen bonds : angle 4.73507 ( 5172) link_TRANS : bond 0.00031 ( 4) link_TRANS : angle 0.30234 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.766 Fit side-chains REVERT: A 525 TRP cc_start: 0.8086 (t60) cc_final: 0.7809 (t60) REVERT: A 741 ASN cc_start: 0.8857 (m-40) cc_final: 0.8646 (t0) REVERT: A 752 PHE cc_start: 0.8484 (t80) cc_final: 0.8221 (t80) REVERT: B 189 MET cc_start: 0.8381 (mmm) cc_final: 0.8148 (mmm) REVERT: B 525 TRP cc_start: 0.7969 (t60) cc_final: 0.7756 (t60) REVERT: B 741 ASN cc_start: 0.8830 (m-40) cc_final: 0.8561 (t0) REVERT: B 752 PHE cc_start: 0.8493 (t80) cc_final: 0.8122 (t80) REVERT: B 895 TRP cc_start: 0.7726 (m-90) cc_final: 0.6240 (p-90) REVERT: B 955 THR cc_start: 0.8346 (t) cc_final: 0.8144 (t) REVERT: C 189 MET cc_start: 0.8389 (mmm) cc_final: 0.8155 (mmm) REVERT: C 525 TRP cc_start: 0.7949 (t60) cc_final: 0.7745 (t60) REVERT: C 741 ASN cc_start: 0.8830 (m-40) cc_final: 0.8560 (t0) REVERT: C 752 PHE cc_start: 0.8493 (t80) cc_final: 0.8128 (t80) REVERT: C 895 TRP cc_start: 0.7725 (m-90) cc_final: 0.6238 (p-90) REVERT: C 955 THR cc_start: 0.8370 (t) cc_final: 0.8165 (t) REVERT: D 189 MET cc_start: 0.8390 (mmm) cc_final: 0.8154 (mmm) REVERT: D 525 TRP cc_start: 0.7970 (t60) cc_final: 0.7756 (t60) REVERT: D 741 ASN cc_start: 0.8830 (m-40) cc_final: 0.8562 (t0) REVERT: D 752 PHE cc_start: 0.8496 (t80) cc_final: 0.8125 (t80) REVERT: D 895 TRP cc_start: 0.7742 (m-90) cc_final: 0.6246 (p-90) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1244 time to fit residues: 75.2583 Evaluate side-chains 254 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104833 restraints weight = 77402.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104873 restraints weight = 78046.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105534 restraints weight = 59820.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105780 restraints weight = 45941.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105828 restraints weight = 44580.665| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22868 Z= 0.157 Angle : 0.550 6.300 31404 Z= 0.293 Chirality : 0.040 0.167 3868 Planarity : 0.005 0.065 3940 Dihedral : 4.722 21.090 3412 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.15), residues: 2952 helix: 0.91 (0.11), residues: 2268 sheet: -3.58 (0.62), residues: 40 loop : -1.55 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 532 TYR 0.036 0.002 TYR D 772 PHE 0.018 0.002 PHE A 629 TRP 0.035 0.001 TRP B 993 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00340 (22864) covalent geometry : angle 0.54989 (31392) hydrogen bonds : bond 0.03671 ( 1728) hydrogen bonds : angle 4.25765 ( 5172) link_TRANS : bond 0.00135 ( 4) link_TRANS : angle 0.27254 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.680 Fit side-chains REVERT: A 525 TRP cc_start: 0.8143 (t60) cc_final: 0.7837 (t60) REVERT: A 615 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 741 ASN cc_start: 0.8877 (m-40) cc_final: 0.8654 (t0) REVERT: A 965 SER cc_start: 0.7816 (m) cc_final: 0.7189 (p) REVERT: A 971 VAL cc_start: 0.8941 (t) cc_final: 0.8694 (p) REVERT: B 189 MET cc_start: 0.8036 (mmm) cc_final: 0.7833 (mmm) REVERT: B 525 TRP cc_start: 0.8165 (t60) cc_final: 0.7837 (t60) REVERT: B 741 ASN cc_start: 0.8854 (m-40) cc_final: 0.8607 (t0) REVERT: B 895 TRP cc_start: 0.7668 (m-90) cc_final: 0.6311 (p-90) REVERT: B 965 SER cc_start: 0.7779 (m) cc_final: 0.7169 (p) REVERT: B 971 VAL cc_start: 0.9008 (t) cc_final: 0.8799 (p) REVERT: C 189 MET cc_start: 0.8038 (mmm) cc_final: 0.7835 (mmm) REVERT: C 525 TRP cc_start: 0.8171 (t60) cc_final: 0.7842 (t60) REVERT: C 741 ASN cc_start: 0.8848 (m-40) cc_final: 0.8605 (t0) REVERT: C 895 TRP cc_start: 0.7672 (m-90) cc_final: 0.6306 (p-90) REVERT: C 965 SER cc_start: 0.7769 (m) cc_final: 0.7154 (p) REVERT: C 971 VAL cc_start: 0.9019 (t) cc_final: 0.8818 (p) REVERT: D 189 MET cc_start: 0.8027 (mmm) cc_final: 0.7825 (mmm) REVERT: D 525 TRP cc_start: 0.8165 (t60) cc_final: 0.7844 (t60) REVERT: D 741 ASN cc_start: 0.8853 (m-40) cc_final: 0.8612 (t0) REVERT: D 895 TRP cc_start: 0.7711 (m-90) cc_final: 0.6322 (p-90) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1200 time to fit residues: 70.5050 Evaluate side-chains 248 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 234 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099363 restraints weight = 78023.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100528 restraints weight = 57424.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100647 restraints weight = 42648.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100822 restraints weight = 41621.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100866 restraints weight = 39839.199| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22868 Z= 0.221 Angle : 0.629 7.502 31404 Z= 0.331 Chirality : 0.042 0.164 3868 Planarity : 0.005 0.062 3940 Dihedral : 4.782 21.828 3412 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2952 helix: 1.18 (0.11), residues: 2260 sheet: -2.64 (0.50), residues: 76 loop : -1.46 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 532 TYR 0.008 0.001 TYR C 295 PHE 0.024 0.002 PHE B 776 TRP 0.044 0.002 TRP B 993 HIS 0.007 0.002 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00488 (22864) covalent geometry : angle 0.62874 (31392) hydrogen bonds : bond 0.03975 ( 1728) hydrogen bonds : angle 4.37231 ( 5172) link_TRANS : bond 0.00116 ( 4) link_TRANS : angle 0.15396 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.837 Fit side-chains REVERT: A 358 LEU cc_start: 0.7843 (mt) cc_final: 0.7614 (tt) REVERT: A 525 TRP cc_start: 0.8134 (t60) cc_final: 0.7820 (t60) REVERT: A 741 ASN cc_start: 0.8931 (m-40) cc_final: 0.8636 (t0) REVERT: A 965 SER cc_start: 0.7888 (m) cc_final: 0.7248 (p) REVERT: B 525 TRP cc_start: 0.8127 (t60) cc_final: 0.7786 (t60) REVERT: B 741 ASN cc_start: 0.8923 (m-40) cc_final: 0.8587 (t0) REVERT: B 895 TRP cc_start: 0.8058 (m-90) cc_final: 0.6497 (p-90) REVERT: B 965 SER cc_start: 0.7727 (m) cc_final: 0.7153 (p) REVERT: C 525 TRP cc_start: 0.8128 (t60) cc_final: 0.7790 (t60) REVERT: C 741 ASN cc_start: 0.8917 (m-40) cc_final: 0.8585 (t0) REVERT: C 895 TRP cc_start: 0.8061 (m-90) cc_final: 0.6500 (p-90) REVERT: C 965 SER cc_start: 0.7734 (m) cc_final: 0.7179 (p) REVERT: D 525 TRP cc_start: 0.8129 (t60) cc_final: 0.7794 (t60) REVERT: D 741 ASN cc_start: 0.8928 (m-40) cc_final: 0.8588 (t0) REVERT: D 895 TRP cc_start: 0.8071 (m-90) cc_final: 0.6510 (p-90) REVERT: D 965 SER cc_start: 0.7710 (m) cc_final: 0.7008 (p) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1083 time to fit residues: 58.1154 Evaluate side-chains 243 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 288 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.117433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102547 restraints weight = 76903.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101906 restraints weight = 84390.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102485 restraints weight = 65528.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102655 restraints weight = 51717.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102861 restraints weight = 48996.279| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22868 Z= 0.203 Angle : 0.582 6.764 31404 Z= 0.311 Chirality : 0.041 0.163 3868 Planarity : 0.004 0.062 3940 Dihedral : 4.665 20.425 3412 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2952 helix: 1.34 (0.11), residues: 2264 sheet: -2.28 (0.54), residues: 76 loop : -1.55 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 532 TYR 0.015 0.001 TYR A 772 PHE 0.024 0.002 PHE A 776 TRP 0.048 0.002 TRP B 993 HIS 0.005 0.001 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00442 (22864) covalent geometry : angle 0.58228 (31392) hydrogen bonds : bond 0.03763 ( 1728) hydrogen bonds : angle 4.27193 ( 5172) link_TRANS : bond 0.00096 ( 4) link_TRANS : angle 0.16659 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.934 Fit side-chains REVERT: A 525 TRP cc_start: 0.8088 (t60) cc_final: 0.7768 (t60) REVERT: A 601 MET cc_start: 0.7698 (tmm) cc_final: 0.7493 (tmm) REVERT: A 741 ASN cc_start: 0.8894 (m-40) cc_final: 0.8523 (t0) REVERT: A 895 TRP cc_start: 0.7893 (m-90) cc_final: 0.6535 (p-90) REVERT: A 965 SER cc_start: 0.7738 (m) cc_final: 0.7201 (p) REVERT: B 525 TRP cc_start: 0.8123 (t60) cc_final: 0.7779 (t60) REVERT: B 601 MET cc_start: 0.7651 (tmm) cc_final: 0.7441 (tmm) REVERT: B 741 ASN cc_start: 0.8843 (m-40) cc_final: 0.8454 (t0) REVERT: B 895 TRP cc_start: 0.7860 (m-90) cc_final: 0.6489 (p-90) REVERT: B 965 SER cc_start: 0.7738 (m) cc_final: 0.7166 (p) REVERT: C 525 TRP cc_start: 0.8102 (t60) cc_final: 0.7756 (t60) REVERT: C 601 MET cc_start: 0.7696 (tmm) cc_final: 0.7486 (tmm) REVERT: C 741 ASN cc_start: 0.8836 (m-40) cc_final: 0.8457 (t0) REVERT: C 895 TRP cc_start: 0.7872 (m-90) cc_final: 0.6495 (p-90) REVERT: C 965 SER cc_start: 0.7727 (m) cc_final: 0.7181 (p) REVERT: D 525 TRP cc_start: 0.8125 (t60) cc_final: 0.7789 (t60) REVERT: D 601 MET cc_start: 0.7694 (tmm) cc_final: 0.7481 (tmm) REVERT: D 741 ASN cc_start: 0.8840 (m-40) cc_final: 0.8453 (t0) REVERT: D 895 TRP cc_start: 0.7893 (m-90) cc_final: 0.6500 (p-90) REVERT: D 965 SER cc_start: 0.7489 (m) cc_final: 0.6848 (p) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1261 time to fit residues: 72.0680 Evaluate side-chains 247 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 201 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102899 restraints weight = 77394.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102753 restraints weight = 72427.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103272 restraints weight = 61550.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103518 restraints weight = 48841.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103588 restraints weight = 45972.237| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22868 Z= 0.167 Angle : 0.554 7.268 31404 Z= 0.294 Chirality : 0.041 0.175 3868 Planarity : 0.004 0.062 3940 Dihedral : 4.513 21.391 3412 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.16), residues: 2952 helix: 1.51 (0.11), residues: 2264 sheet: -4.70 (0.36), residues: 48 loop : -1.35 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 532 TYR 0.007 0.001 TYR D 497 PHE 0.026 0.002 PHE A 629 TRP 0.053 0.002 TRP B 993 HIS 0.005 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00374 (22864) covalent geometry : angle 0.55424 (31392) hydrogen bonds : bond 0.03555 ( 1728) hydrogen bonds : angle 4.10285 ( 5172) link_TRANS : bond 0.00085 ( 4) link_TRANS : angle 0.13275 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.913 Fit side-chains REVERT: A 525 TRP cc_start: 0.8079 (t60) cc_final: 0.7757 (t60) REVERT: A 741 ASN cc_start: 0.8870 (m-40) cc_final: 0.8492 (t0) REVERT: A 895 TRP cc_start: 0.7912 (m-90) cc_final: 0.6551 (p-90) REVERT: A 965 SER cc_start: 0.7598 (m) cc_final: 0.7021 (p) REVERT: B 525 TRP cc_start: 0.8124 (t60) cc_final: 0.7761 (t60) REVERT: B 741 ASN cc_start: 0.8875 (m-40) cc_final: 0.8456 (t0) REVERT: B 895 TRP cc_start: 0.7865 (m-90) cc_final: 0.6508 (p-90) REVERT: B 965 SER cc_start: 0.7551 (m) cc_final: 0.6939 (p) REVERT: C 525 TRP cc_start: 0.8135 (t60) cc_final: 0.7778 (t60) REVERT: C 741 ASN cc_start: 0.8869 (m-40) cc_final: 0.8460 (t0) REVERT: C 895 TRP cc_start: 0.7881 (m-90) cc_final: 0.6514 (p-90) REVERT: C 965 SER cc_start: 0.7525 (m) cc_final: 0.6960 (p) REVERT: D 525 TRP cc_start: 0.8126 (t60) cc_final: 0.7774 (t60) REVERT: D 741 ASN cc_start: 0.8866 (m-40) cc_final: 0.8459 (t0) REVERT: D 895 TRP cc_start: 0.7896 (m-90) cc_final: 0.6524 (p-90) REVERT: D 965 SER cc_start: 0.7290 (m) cc_final: 0.6737 (p) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1254 time to fit residues: 70.6311 Evaluate side-chains 250 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 294 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.113509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097542 restraints weight = 78532.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097682 restraints weight = 75773.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098645 restraints weight = 60556.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098445 restraints weight = 47672.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098559 restraints weight = 47604.192| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 22868 Z= 0.347 Angle : 0.778 8.442 31404 Z= 0.410 Chirality : 0.047 0.179 3868 Planarity : 0.005 0.060 3940 Dihedral : 5.230 26.443 3412 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 2952 helix: 0.93 (0.11), residues: 2228 sheet: -5.31 (0.31), residues: 40 loop : -1.67 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 997 TYR 0.030 0.002 TYR A 497 PHE 0.024 0.002 PHE A 629 TRP 0.055 0.003 TRP B 993 HIS 0.007 0.002 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00760 (22864) covalent geometry : angle 0.77799 (31392) hydrogen bonds : bond 0.04661 ( 1728) hydrogen bonds : angle 4.92000 ( 5172) link_TRANS : bond 0.00127 ( 4) link_TRANS : angle 0.24846 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.871 Fit side-chains REVERT: A 189 MET cc_start: 0.8250 (mmm) cc_final: 0.8016 (mmm) REVERT: A 525 TRP cc_start: 0.8159 (t60) cc_final: 0.7866 (t60) REVERT: A 741 ASN cc_start: 0.8922 (m-40) cc_final: 0.8382 (t0) REVERT: A 965 SER cc_start: 0.7928 (m) cc_final: 0.7341 (p) REVERT: B 525 TRP cc_start: 0.8162 (t60) cc_final: 0.7790 (t60) REVERT: B 741 ASN cc_start: 0.8929 (m-40) cc_final: 0.8384 (t0) REVERT: B 776 PHE cc_start: 0.7697 (m-80) cc_final: 0.7256 (m-80) REVERT: B 895 TRP cc_start: 0.7888 (m-90) cc_final: 0.6482 (p-90) REVERT: B 965 SER cc_start: 0.7835 (m) cc_final: 0.7234 (p) REVERT: C 525 TRP cc_start: 0.8126 (t60) cc_final: 0.7796 (t60) REVERT: C 741 ASN cc_start: 0.8919 (m-40) cc_final: 0.8385 (t0) REVERT: C 776 PHE cc_start: 0.7693 (m-80) cc_final: 0.7250 (m-80) REVERT: C 895 TRP cc_start: 0.7873 (m-90) cc_final: 0.6431 (p-90) REVERT: C 965 SER cc_start: 0.7851 (m) cc_final: 0.7287 (p) REVERT: D 525 TRP cc_start: 0.8159 (t60) cc_final: 0.7798 (t60) REVERT: D 741 ASN cc_start: 0.8915 (m-40) cc_final: 0.8381 (t0) REVERT: D 776 PHE cc_start: 0.7694 (m-80) cc_final: 0.7256 (m-80) REVERT: D 895 TRP cc_start: 0.7903 (m-90) cc_final: 0.6449 (p-90) REVERT: D 965 SER cc_start: 0.7635 (m) cc_final: 0.7002 (p) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1261 time to fit residues: 62.1534 Evaluate side-chains 215 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 267 optimal weight: 5.9990 chunk 299 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104095 restraints weight = 76664.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103746 restraints weight = 79759.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104392 restraints weight = 65729.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104753 restraints weight = 48660.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104843 restraints weight = 46233.720| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22868 Z= 0.134 Angle : 0.548 8.338 31404 Z= 0.288 Chirality : 0.040 0.148 3868 Planarity : 0.004 0.064 3940 Dihedral : 4.572 22.178 3412 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 2952 helix: 1.53 (0.11), residues: 2264 sheet: -3.00 (0.46), residues: 104 loop : -1.63 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 532 TYR 0.026 0.001 TYR A 772 PHE 0.021 0.001 PHE D 629 TRP 0.054 0.002 TRP B 993 HIS 0.005 0.001 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00296 (22864) covalent geometry : angle 0.54816 (31392) hydrogen bonds : bond 0.03520 ( 1728) hydrogen bonds : angle 4.08126 ( 5172) link_TRANS : bond 0.00114 ( 4) link_TRANS : angle 0.16418 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.892 Fit side-chains REVERT: A 525 TRP cc_start: 0.8143 (t60) cc_final: 0.7860 (t60) REVERT: A 601 MET cc_start: 0.7656 (tmm) cc_final: 0.7346 (tmm) REVERT: A 741 ASN cc_start: 0.8892 (m-40) cc_final: 0.8443 (t0) REVERT: A 895 TRP cc_start: 0.7876 (m-90) cc_final: 0.6528 (p-90) REVERT: A 965 SER cc_start: 0.7659 (m) cc_final: 0.7046 (p) REVERT: B 525 TRP cc_start: 0.8102 (t60) cc_final: 0.7765 (t60) REVERT: B 601 MET cc_start: 0.7640 (tmm) cc_final: 0.7315 (tmm) REVERT: B 741 ASN cc_start: 0.8909 (m-40) cc_final: 0.8443 (t0) REVERT: B 895 TRP cc_start: 0.7803 (m-90) cc_final: 0.6532 (p-90) REVERT: B 965 SER cc_start: 0.7496 (m) cc_final: 0.6920 (p) REVERT: C 525 TRP cc_start: 0.8090 (t60) cc_final: 0.7751 (t60) REVERT: C 601 MET cc_start: 0.7659 (tmm) cc_final: 0.7324 (tmm) REVERT: C 741 ASN cc_start: 0.8904 (m-40) cc_final: 0.8447 (t0) REVERT: C 895 TRP cc_start: 0.7826 (m-90) cc_final: 0.6537 (p-90) REVERT: C 965 SER cc_start: 0.7541 (m) cc_final: 0.6971 (p) REVERT: D 525 TRP cc_start: 0.8062 (t60) cc_final: 0.7739 (t60) REVERT: D 601 MET cc_start: 0.7641 (tmm) cc_final: 0.7306 (tmm) REVERT: D 741 ASN cc_start: 0.8899 (m-40) cc_final: 0.8439 (t0) REVERT: D 895 TRP cc_start: 0.7845 (m-90) cc_final: 0.6547 (p-90) REVERT: D 965 SER cc_start: 0.7611 (m) cc_final: 0.7156 (p) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.1220 time to fit residues: 68.5711 Evaluate side-chains 234 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 57 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 0.0000 chunk 233 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.114696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099349 restraints weight = 78026.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098704 restraints weight = 75715.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099258 restraints weight = 77011.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099513 restraints weight = 54820.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099623 restraints weight = 50618.878| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22868 Z= 0.292 Angle : 0.712 8.619 31404 Z= 0.378 Chirality : 0.045 0.182 3868 Planarity : 0.005 0.065 3940 Dihedral : 4.978 23.619 3412 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2952 helix: 1.15 (0.11), residues: 2256 sheet: -3.08 (0.49), residues: 84 loop : -1.79 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 997 TYR 0.026 0.002 TYR B 497 PHE 0.026 0.002 PHE A 629 TRP 0.054 0.002 TRP C 993 HIS 0.006 0.002 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00643 (22864) covalent geometry : angle 0.71169 (31392) hydrogen bonds : bond 0.04316 ( 1728) hydrogen bonds : angle 4.61485 ( 5172) link_TRANS : bond 0.00106 ( 4) link_TRANS : angle 0.21035 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.902 Fit side-chains REVERT: A 741 ASN cc_start: 0.8928 (m-40) cc_final: 0.8398 (t0) REVERT: A 895 TRP cc_start: 0.8007 (m-90) cc_final: 0.6568 (p-90) REVERT: A 965 SER cc_start: 0.7754 (m) cc_final: 0.7159 (p) REVERT: B 525 TRP cc_start: 0.8135 (t60) cc_final: 0.7792 (t60) REVERT: B 741 ASN cc_start: 0.8935 (m-40) cc_final: 0.8372 (t0) REVERT: B 776 PHE cc_start: 0.7798 (m-80) cc_final: 0.7388 (m-80) REVERT: B 895 TRP cc_start: 0.7977 (m-90) cc_final: 0.6514 (p-90) REVERT: B 965 SER cc_start: 0.7639 (m) cc_final: 0.7051 (p) REVERT: C 525 TRP cc_start: 0.8108 (t60) cc_final: 0.7799 (t60) REVERT: C 741 ASN cc_start: 0.8927 (m-40) cc_final: 0.8377 (t0) REVERT: C 776 PHE cc_start: 0.7807 (m-80) cc_final: 0.7395 (m-80) REVERT: C 895 TRP cc_start: 0.7987 (m-90) cc_final: 0.6518 (p-90) REVERT: C 965 SER cc_start: 0.7683 (m) cc_final: 0.7111 (p) REVERT: D 525 TRP cc_start: 0.8128 (t60) cc_final: 0.7790 (t60) REVERT: D 741 ASN cc_start: 0.8933 (m-40) cc_final: 0.8377 (t0) REVERT: D 776 PHE cc_start: 0.7792 (m-80) cc_final: 0.7382 (m-80) REVERT: D 895 TRP cc_start: 0.8019 (m-90) cc_final: 0.6530 (p-90) REVERT: D 904 TYR cc_start: 0.5294 (m-10) cc_final: 0.4535 (m-80) REVERT: D 965 SER cc_start: 0.7594 (m) cc_final: 0.6984 (p) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1243 time to fit residues: 62.5671 Evaluate side-chains 217 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 98 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 289 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102571 restraints weight = 77099.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103100 restraints weight = 70737.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104081 restraints weight = 49968.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104002 restraints weight = 39131.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104057 restraints weight = 38698.147| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22868 Z= 0.129 Angle : 0.547 6.292 31404 Z= 0.290 Chirality : 0.040 0.185 3868 Planarity : 0.004 0.067 3940 Dihedral : 4.519 22.252 3412 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.16), residues: 2952 helix: 1.60 (0.11), residues: 2264 sheet: -2.63 (0.49), residues: 84 loop : -1.88 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.043 0.002 TYR D 772 PHE 0.027 0.002 PHE D 838 TRP 0.047 0.002 TRP B 993 HIS 0.006 0.001 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00287 (22864) covalent geometry : angle 0.54686 (31392) hydrogen bonds : bond 0.03460 ( 1728) hydrogen bonds : angle 4.04349 ( 5172) link_TRANS : bond 0.00100 ( 4) link_TRANS : angle 0.17426 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.877 Fit side-chains REVERT: A 525 TRP cc_start: 0.8156 (t60) cc_final: 0.7847 (t60) REVERT: A 615 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 741 ASN cc_start: 0.8928 (m-40) cc_final: 0.8485 (t0) REVERT: A 965 SER cc_start: 0.7824 (m) cc_final: 0.7359 (p) REVERT: B 525 TRP cc_start: 0.8086 (t60) cc_final: 0.7742 (t60) REVERT: B 741 ASN cc_start: 0.8912 (m-40) cc_final: 0.8482 (t0) REVERT: B 895 TRP cc_start: 0.7972 (m-90) cc_final: 0.6604 (p-90) REVERT: B 965 SER cc_start: 0.7729 (m) cc_final: 0.7247 (p) REVERT: C 525 TRP cc_start: 0.8109 (t60) cc_final: 0.7763 (t60) REVERT: C 741 ASN cc_start: 0.8908 (m-40) cc_final: 0.8486 (t0) REVERT: C 776 PHE cc_start: 0.7859 (m-80) cc_final: 0.7653 (m-80) REVERT: C 895 TRP cc_start: 0.7983 (m-90) cc_final: 0.6611 (p-90) REVERT: C 965 SER cc_start: 0.7742 (m) cc_final: 0.7250 (p) REVERT: D 525 TRP cc_start: 0.8094 (t60) cc_final: 0.7753 (t60) REVERT: D 741 ASN cc_start: 0.8906 (m-40) cc_final: 0.8477 (t0) REVERT: D 895 TRP cc_start: 0.8028 (m-90) cc_final: 0.6607 (p-90) REVERT: D 904 TYR cc_start: 0.5920 (m-10) cc_final: 0.5319 (m-80) REVERT: D 965 SER cc_start: 0.7504 (m) cc_final: 0.7046 (p) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1226 time to fit residues: 66.7806 Evaluate side-chains 234 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 62 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 193 optimal weight: 0.0050 chunk 69 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099065 restraints weight = 78257.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098287 restraints weight = 75175.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098877 restraints weight = 75076.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099014 restraints weight = 55726.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099148 restraints weight = 52256.174| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22868 Z= 0.294 Angle : 0.715 8.396 31404 Z= 0.379 Chirality : 0.045 0.172 3868 Planarity : 0.005 0.066 3940 Dihedral : 4.961 23.480 3412 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 2952 helix: 1.19 (0.11), residues: 2264 sheet: -3.03 (0.48), residues: 84 loop : -1.90 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 997 TYR 0.034 0.002 TYR B 835 PHE 0.026 0.002 PHE A 629 TRP 0.042 0.002 TRP A 993 HIS 0.006 0.002 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00649 (22864) covalent geometry : angle 0.71464 (31392) hydrogen bonds : bond 0.04286 ( 1728) hydrogen bonds : angle 4.58276 ( 5172) link_TRANS : bond 0.00084 ( 4) link_TRANS : angle 0.20168 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.90 seconds wall clock time: 51 minutes 49.10 seconds (3109.10 seconds total)