Starting phenix.real_space_refine on Thu Jun 19 16:30:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bpq_7127/06_2025/6bpq_7127_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bpq_7127/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6bpq_7127/06_2025/6bpq_7127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bpq_7127/06_2025/6bpq_7127.map" model { file = "/net/cci-nas-00/data/ceres_data/6bpq_7127/06_2025/6bpq_7127_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bpq_7127/06_2025/6bpq_7127_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'UNK:plan-1': 20, 'HIS:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP: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: {'GLN:plan1': 15, 'HIS:plan': 1, 'ASN:plan1': 18, 'TYR:plan': 5, 'UNK:plan-1': 5, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 7, 'GLU:plan': 38, 'ARG:plan': 19} 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: {'GLU:plan': 4, 'UNK:plan-1': 18, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG: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: C, B, D Time building chain proxies: 13.04, per 1000 atoms: 0.58 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: 6.22 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.97 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: 7.91 Time building geometry restraints manager: 7.24 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 52.390 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.042 0.003 TRP B 993 HIS 0.009 0.003 HIS B 259 PHE 0.043 0.003 PHE B 867 TYR 0.027 0.003 TYR A 772 ARG 0.006 0.001 ARG D 532 Details of bonding type rmsd link_TRANS : bond 0.00223 ( 4) link_TRANS : angle 0.80445 ( 12) hydrogen bonds : bond 0.14059 ( 1728) hydrogen bonds : angle 6.52315 ( 5172) covalent geometry : bond 0.00662 (22864) covalent geometry : angle 0.91787 (31392) *********************** 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 : 2.344 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: 0.2859 time to fit residues: 229.4895 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 : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.116407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099228 restraints weight = 77618.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100165 restraints weight = 55334.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100262 restraints weight = 45456.466| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22868 Z= 0.294 Angle : 0.733 7.153 31404 Z= 0.391 Chirality : 0.044 0.163 3868 Planarity : 0.006 0.066 3940 Dihedral : 5.354 24.368 3412 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 2952 helix: -0.03 (0.10), residues: 2232 sheet: -3.80 (0.67), residues: 40 loop : -1.74 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 993 HIS 0.009 0.002 HIS A 389 PHE 0.018 0.002 PHE A 629 TYR 0.012 0.002 TYR C 295 ARG 0.005 0.001 ARG B 532 Details of bonding type rmsd link_TRANS : bond 0.00031 ( 4) link_TRANS : angle 0.22725 ( 12) hydrogen bonds : bond 0.04470 ( 1728) hydrogen bonds : angle 4.92109 ( 5172) covalent geometry : bond 0.00644 (22864) covalent geometry : angle 0.73314 (31392) *********************** 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 343 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 2.272 Fit side-chains REVERT: A 525 TRP cc_start: 0.8142 (t60) cc_final: 0.7836 (t60) REVERT: A 741 ASN cc_start: 0.8884 (m-40) cc_final: 0.8642 (t0) REVERT: A 752 PHE cc_start: 0.8618 (t80) cc_final: 0.8209 (t80) REVERT: A 772 TYR cc_start: 0.7972 (m-80) cc_final: 0.7655 (m-80) REVERT: A 835 TYR cc_start: 0.8895 (t80) cc_final: 0.8638 (t80) REVERT: B 525 TRP cc_start: 0.8249 (t60) cc_final: 0.7901 (t60) REVERT: B 741 ASN cc_start: 0.8872 (m-40) cc_final: 0.8597 (t0) REVERT: B 752 PHE cc_start: 0.8654 (t80) cc_final: 0.8136 (t80) REVERT: B 772 TYR cc_start: 0.7931 (m-80) cc_final: 0.7622 (m-80) REVERT: B 835 TYR cc_start: 0.8831 (t80) cc_final: 0.8512 (t80) REVERT: B 895 TRP cc_start: 0.7965 (m-90) cc_final: 0.6172 (p-90) REVERT: C 525 TRP cc_start: 0.8226 (t60) cc_final: 0.7894 (t60) REVERT: C 741 ASN cc_start: 0.8866 (m-40) cc_final: 0.8594 (t0) REVERT: C 752 PHE cc_start: 0.8657 (t80) cc_final: 0.8142 (t80) REVERT: C 772 TYR cc_start: 0.7928 (m-80) cc_final: 0.7625 (m-80) REVERT: C 835 TYR cc_start: 0.8828 (t80) cc_final: 0.8498 (t80) REVERT: C 895 TRP cc_start: 0.7962 (m-90) cc_final: 0.6166 (p-90) REVERT: D 525 TRP cc_start: 0.8238 (t60) cc_final: 0.7894 (t60) REVERT: D 741 ASN cc_start: 0.8870 (m-40) cc_final: 0.8594 (t0) REVERT: D 752 PHE cc_start: 0.8660 (t80) cc_final: 0.8149 (t80) REVERT: D 772 TYR cc_start: 0.7929 (m-80) cc_final: 0.7621 (m-80) REVERT: D 835 TYR cc_start: 0.8836 (t80) cc_final: 0.8501 (t80) REVERT: D 895 TRP cc_start: 0.7971 (m-90) cc_final: 0.6174 (p-90) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2938 time to fit residues: 166.8517 Evaluate side-chains 259 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 168 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.115829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101189 restraints weight = 77625.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100815 restraints weight = 80484.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101571 restraints weight = 64525.342| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22868 Z= 0.254 Angle : 0.660 7.795 31404 Z= 0.350 Chirality : 0.042 0.170 3868 Planarity : 0.005 0.065 3940 Dihedral : 5.096 23.026 3412 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2952 helix: 0.70 (0.11), residues: 2256 sheet: -4.43 (0.49), residues: 40 loop : -1.62 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 993 HIS 0.007 0.002 HIS A 389 PHE 0.020 0.002 PHE A 629 TYR 0.011 0.002 TYR D 295 ARG 0.006 0.001 ARG A 532 Details of bonding type rmsd link_TRANS : bond 0.00189 ( 4) link_TRANS : angle 0.30477 ( 12) hydrogen bonds : bond 0.04216 ( 1728) hydrogen bonds : angle 4.65708 ( 5172) covalent geometry : bond 0.00559 (22864) covalent geometry : angle 0.66012 (31392) *********************** 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 308 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.324 Fit side-chains REVERT: A 525 TRP cc_start: 0.8168 (t60) cc_final: 0.7869 (t60) REVERT: A 615 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 741 ASN cc_start: 0.8881 (m-40) cc_final: 0.8572 (t0) REVERT: A 752 PHE cc_start: 0.8516 (t80) cc_final: 0.8118 (t80) REVERT: A 772 TYR cc_start: 0.7876 (m-80) cc_final: 0.7573 (m-80) REVERT: A 776 PHE cc_start: 0.7427 (m-80) cc_final: 0.7034 (m-80) REVERT: A 895 TRP cc_start: 0.7823 (m-90) cc_final: 0.6440 (p-90) REVERT: B 525 TRP cc_start: 0.8128 (t60) cc_final: 0.7803 (t60) REVERT: B 615 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 741 ASN cc_start: 0.8865 (m-40) cc_final: 0.8525 (t0) REVERT: B 752 PHE cc_start: 0.8527 (t80) cc_final: 0.8023 (t80) REVERT: B 772 TYR cc_start: 0.7879 (m-80) cc_final: 0.7579 (m-80) REVERT: B 776 PHE cc_start: 0.7427 (m-80) cc_final: 0.7004 (m-80) REVERT: B 844 HIS cc_start: 0.8961 (t-90) cc_final: 0.8758 (t-90) REVERT: B 895 TRP cc_start: 0.7799 (m-90) cc_final: 0.6223 (p-90) REVERT: C 525 TRP cc_start: 0.8111 (t60) cc_final: 0.7795 (t60) REVERT: C 615 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 741 ASN cc_start: 0.8864 (m-40) cc_final: 0.8523 (t0) REVERT: C 752 PHE cc_start: 0.8524 (t80) cc_final: 0.8017 (t80) REVERT: C 772 TYR cc_start: 0.7882 (m-80) cc_final: 0.7586 (m-80) REVERT: C 776 PHE cc_start: 0.7442 (m-80) cc_final: 0.7015 (m-80) REVERT: C 895 TRP cc_start: 0.7795 (m-90) cc_final: 0.6221 (p-90) REVERT: D 525 TRP cc_start: 0.8122 (t60) cc_final: 0.7799 (t60) REVERT: D 615 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 741 ASN cc_start: 0.8861 (m-40) cc_final: 0.8524 (t0) REVERT: D 752 PHE cc_start: 0.8532 (t80) cc_final: 0.8016 (t80) REVERT: D 772 TYR cc_start: 0.7893 (m-80) cc_final: 0.7592 (m-80) REVERT: D 776 PHE cc_start: 0.7431 (m-80) cc_final: 0.7010 (m-80) REVERT: D 895 TRP cc_start: 0.7810 (m-90) cc_final: 0.6234 (p-90) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2551 time to fit residues: 134.3656 Evaluate side-chains 231 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 223 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.119004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103606 restraints weight = 77873.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103547 restraints weight = 75058.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104090 restraints weight = 59780.937| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22868 Z= 0.138 Angle : 0.529 5.862 31404 Z= 0.281 Chirality : 0.039 0.162 3868 Planarity : 0.004 0.063 3940 Dihedral : 4.592 22.456 3412 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.16), residues: 2952 helix: 1.27 (0.11), residues: 2264 sheet: -2.22 (0.52), residues: 96 loop : -1.45 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 993 HIS 0.004 0.001 HIS A 389 PHE 0.019 0.002 PHE B 629 TYR 0.012 0.001 TYR A 772 ARG 0.004 0.001 ARG D 532 Details of bonding type rmsd link_TRANS : bond 0.00111 ( 4) link_TRANS : angle 0.20269 ( 12) hydrogen bonds : bond 0.03537 ( 1728) hydrogen bonds : angle 4.13541 ( 5172) covalent geometry : bond 0.00302 (22864) covalent geometry : angle 0.52959 (31392) *********************** 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 331 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 2.422 Fit side-chains REVERT: A 358 LEU cc_start: 0.7938 (mt) cc_final: 0.7693 (tt) REVERT: A 525 TRP cc_start: 0.8337 (t60) cc_final: 0.7941 (t60) REVERT: A 601 MET cc_start: 0.7976 (tmm) cc_final: 0.7512 (tmm) REVERT: A 615 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 741 ASN cc_start: 0.8892 (m-40) cc_final: 0.8595 (t0) REVERT: A 772 TYR cc_start: 0.7870 (m-80) cc_final: 0.7663 (m-80) REVERT: A 895 TRP cc_start: 0.7994 (m-90) cc_final: 0.6524 (p-90) REVERT: A 965 SER cc_start: 0.7661 (m) cc_final: 0.7053 (p) REVERT: B 358 LEU cc_start: 0.7927 (mt) cc_final: 0.7680 (tt) REVERT: B 525 TRP cc_start: 0.8386 (t60) cc_final: 0.7944 (t60) REVERT: B 615 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 741 ASN cc_start: 0.8873 (m-40) cc_final: 0.8579 (t0) REVERT: B 772 TYR cc_start: 0.7938 (m-80) cc_final: 0.7700 (m-80) REVERT: B 895 TRP cc_start: 0.8010 (m-90) cc_final: 0.6389 (p-90) REVERT: B 965 SER cc_start: 0.7521 (m) cc_final: 0.6868 (p) REVERT: C 358 LEU cc_start: 0.7919 (mt) cc_final: 0.7674 (tt) REVERT: C 525 TRP cc_start: 0.8375 (t60) cc_final: 0.7940 (t60) REVERT: C 615 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7816 (tm-30) REVERT: C 741 ASN cc_start: 0.8871 (m-40) cc_final: 0.8574 (t0) REVERT: C 772 TYR cc_start: 0.7940 (m-80) cc_final: 0.7701 (m-80) REVERT: C 895 TRP cc_start: 0.8008 (m-90) cc_final: 0.6383 (p-90) REVERT: C 965 SER cc_start: 0.7527 (m) cc_final: 0.6952 (p) REVERT: D 358 LEU cc_start: 0.7925 (mt) cc_final: 0.7681 (tt) REVERT: D 525 TRP cc_start: 0.8384 (t60) cc_final: 0.7950 (t60) REVERT: D 615 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7783 (tm-30) REVERT: D 741 ASN cc_start: 0.8872 (m-40) cc_final: 0.8576 (t0) REVERT: D 772 TYR cc_start: 0.7942 (m-80) cc_final: 0.7701 (m-80) REVERT: D 895 TRP cc_start: 0.7998 (m-90) cc_final: 0.6382 (p-90) REVERT: D 965 SER cc_start: 0.7693 (m) cc_final: 0.7037 (p) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2580 time to fit residues: 148.0524 Evaluate side-chains 252 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.115665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101310 restraints weight = 78201.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100965 restraints weight = 78024.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101729 restraints weight = 63375.838| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 22868 Z= 0.269 Angle : 0.668 7.948 31404 Z= 0.353 Chirality : 0.043 0.175 3868 Planarity : 0.005 0.063 3940 Dihedral : 4.883 23.001 3412 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2952 helix: 1.16 (0.11), residues: 2260 sheet: -4.69 (0.39), residues: 40 loop : -1.45 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 993 HIS 0.006 0.002 HIS A 389 PHE 0.026 0.002 PHE A 629 TYR 0.010 0.001 TYR A 295 ARG 0.005 0.001 ARG B 278 Details of bonding type rmsd link_TRANS : bond 0.00125 ( 4) link_TRANS : angle 0.19782 ( 12) hydrogen bonds : bond 0.04115 ( 1728) hydrogen bonds : angle 4.48678 ( 5172) covalent geometry : bond 0.00599 (22864) covalent geometry : angle 0.66784 (31392) *********************** 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 315 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 2.337 Fit side-chains REVERT: A 525 TRP cc_start: 0.8114 (t60) cc_final: 0.7790 (t60) REVERT: A 601 MET cc_start: 0.7726 (tmm) cc_final: 0.7522 (tmm) REVERT: A 615 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 741 ASN cc_start: 0.8920 (m-40) cc_final: 0.8489 (t0) REVERT: A 772 TYR cc_start: 0.7968 (m-80) cc_final: 0.7674 (m-80) REVERT: A 776 PHE cc_start: 0.7411 (m-80) cc_final: 0.7026 (m-80) REVERT: A 895 TRP cc_start: 0.7891 (m-90) cc_final: 0.6488 (p-90) REVERT: A 965 SER cc_start: 0.7991 (m) cc_final: 0.7344 (p) REVERT: B 525 TRP cc_start: 0.8130 (t60) cc_final: 0.7788 (t60) REVERT: B 615 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 741 ASN cc_start: 0.8895 (m-40) cc_final: 0.8460 (t0) REVERT: B 772 TYR cc_start: 0.7936 (m-80) cc_final: 0.7673 (m-80) REVERT: B 776 PHE cc_start: 0.7511 (m-80) cc_final: 0.7143 (m-80) REVERT: B 895 TRP cc_start: 0.7905 (m-90) cc_final: 0.6469 (p-90) REVERT: B 965 SER cc_start: 0.7697 (m) cc_final: 0.7005 (p) REVERT: C 525 TRP cc_start: 0.8109 (t60) cc_final: 0.7775 (t60) REVERT: C 615 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 741 ASN cc_start: 0.8889 (m-40) cc_final: 0.8448 (t0) REVERT: C 772 TYR cc_start: 0.7944 (m-80) cc_final: 0.7676 (m-80) REVERT: C 776 PHE cc_start: 0.7525 (m-80) cc_final: 0.7153 (m-80) REVERT: C 895 TRP cc_start: 0.7898 (m-90) cc_final: 0.6462 (p-90) REVERT: C 965 SER cc_start: 0.7858 (m) cc_final: 0.7236 (p) REVERT: D 525 TRP cc_start: 0.8117 (t60) cc_final: 0.7780 (t60) REVERT: D 615 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7584 (tm-30) REVERT: D 741 ASN cc_start: 0.8897 (m-40) cc_final: 0.8454 (t0) REVERT: D 772 TYR cc_start: 0.7951 (m-80) cc_final: 0.7681 (m-80) REVERT: D 776 PHE cc_start: 0.7514 (m-80) cc_final: 0.7144 (m-80) REVERT: D 895 TRP cc_start: 0.7903 (m-90) cc_final: 0.6469 (p-90) REVERT: D 965 SER cc_start: 0.8049 (m) cc_final: 0.7288 (p) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2719 time to fit residues: 143.7000 Evaluate side-chains 246 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 229 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 257 optimal weight: 0.0010 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.120446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104150 restraints weight = 76424.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104428 restraints weight = 55603.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104338 restraints weight = 46840.639| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22868 Z= 0.110 Angle : 0.497 6.719 31404 Z= 0.263 Chirality : 0.039 0.152 3868 Planarity : 0.004 0.064 3940 Dihedral : 4.371 22.739 3412 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.16), residues: 2952 helix: 1.63 (0.11), residues: 2264 sheet: -2.48 (0.49), residues: 104 loop : -1.43 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 993 HIS 0.005 0.001 HIS D 844 PHE 0.022 0.002 PHE A 629 TYR 0.013 0.001 TYR B 772 ARG 0.004 0.000 ARG B 532 Details of bonding type rmsd link_TRANS : bond 0.00087 ( 4) link_TRANS : angle 0.19174 ( 12) hydrogen bonds : bond 0.03306 ( 1728) hydrogen bonds : angle 3.88695 ( 5172) covalent geometry : bond 0.00237 (22864) covalent geometry : angle 0.49736 (31392) *********************** 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 345 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 2.268 Fit side-chains REVERT: A 525 TRP cc_start: 0.8219 (t60) cc_final: 0.7923 (t60) REVERT: A 615 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 741 ASN cc_start: 0.8911 (m-40) cc_final: 0.8609 (t0) REVERT: A 895 TRP cc_start: 0.8083 (m-90) cc_final: 0.6624 (p-90) REVERT: A 965 SER cc_start: 0.7440 (m) cc_final: 0.6849 (p) REVERT: B 525 TRP cc_start: 0.8166 (t60) cc_final: 0.7787 (t60) REVERT: B 601 MET cc_start: 0.7463 (tmm) cc_final: 0.7162 (tmm) REVERT: B 741 ASN cc_start: 0.8873 (m-40) cc_final: 0.8551 (t0) REVERT: B 895 TRP cc_start: 0.8079 (m-90) cc_final: 0.6607 (p-90) REVERT: B 965 SER cc_start: 0.7389 (m) cc_final: 0.6823 (p) REVERT: C 525 TRP cc_start: 0.8149 (t60) cc_final: 0.7780 (t60) REVERT: C 741 ASN cc_start: 0.8864 (m-40) cc_final: 0.8543 (t0) REVERT: C 895 TRP cc_start: 0.8085 (m-90) cc_final: 0.6606 (p-90) REVERT: C 965 SER cc_start: 0.7345 (m) cc_final: 0.6810 (p) REVERT: D 525 TRP cc_start: 0.8159 (t60) cc_final: 0.7784 (t60) REVERT: D 741 ASN cc_start: 0.8870 (m-40) cc_final: 0.8548 (t0) REVERT: D 772 TYR cc_start: 0.7837 (m-80) cc_final: 0.7566 (m-80) REVERT: D 895 TRP cc_start: 0.8083 (m-90) cc_final: 0.6605 (p-90) REVERT: D 965 SER cc_start: 0.7635 (m) cc_final: 0.7042 (p) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2590 time to fit residues: 152.5465 Evaluate side-chains 258 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 300 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 170 optimal weight: 0.0070 chunk 100 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.117528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102758 restraints weight = 77269.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102387 restraints weight = 76792.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102905 restraints weight = 62698.649| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22868 Z= 0.197 Angle : 0.575 7.593 31404 Z= 0.305 Chirality : 0.041 0.153 3868 Planarity : 0.004 0.063 3940 Dihedral : 4.429 19.210 3412 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2952 helix: 1.57 (0.11), residues: 2260 sheet: -2.59 (0.49), residues: 104 loop : -1.40 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 993 HIS 0.003 0.001 HIS A 389 PHE 0.024 0.002 PHE A 629 TYR 0.012 0.001 TYR A 497 ARG 0.004 0.001 ARG A 278 Details of bonding type rmsd link_TRANS : bond 0.00065 ( 4) link_TRANS : angle 0.11391 ( 12) hydrogen bonds : bond 0.03578 ( 1728) hydrogen bonds : angle 4.05547 ( 5172) covalent geometry : bond 0.00443 (22864) covalent geometry : angle 0.57478 (31392) *********************** 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 312 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 2.648 Fit side-chains REVERT: A 525 TRP cc_start: 0.8083 (t60) cc_final: 0.7824 (t60) REVERT: A 601 MET cc_start: 0.7569 (tmm) cc_final: 0.7352 (tmm) REVERT: A 615 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 741 ASN cc_start: 0.8944 (m-40) cc_final: 0.8498 (t0) REVERT: A 772 TYR cc_start: 0.7659 (m-80) cc_final: 0.7330 (m-80) REVERT: A 895 TRP cc_start: 0.7867 (m-90) cc_final: 0.6511 (p-90) REVERT: A 965 SER cc_start: 0.7648 (m) cc_final: 0.7098 (p) REVERT: B 525 TRP cc_start: 0.8162 (t60) cc_final: 0.7803 (t60) REVERT: B 741 ASN cc_start: 0.8935 (m-40) cc_final: 0.8442 (t0) REVERT: B 772 TYR cc_start: 0.7655 (m-80) cc_final: 0.7421 (m-80) REVERT: B 895 TRP cc_start: 0.7866 (m-90) cc_final: 0.6513 (p-90) REVERT: B 965 SER cc_start: 0.7502 (m) cc_final: 0.6963 (p) REVERT: C 525 TRP cc_start: 0.8123 (t60) cc_final: 0.7791 (t60) REVERT: C 601 MET cc_start: 0.7649 (tmm) cc_final: 0.7434 (tmm) REVERT: C 741 ASN cc_start: 0.8931 (m-40) cc_final: 0.8431 (t0) REVERT: C 772 TYR cc_start: 0.7658 (m-80) cc_final: 0.7422 (m-80) REVERT: C 895 TRP cc_start: 0.7869 (m-90) cc_final: 0.6514 (p-90) REVERT: C 965 SER cc_start: 0.7458 (m) cc_final: 0.6891 (p) REVERT: D 525 TRP cc_start: 0.8148 (t60) cc_final: 0.7799 (t60) REVERT: D 601 MET cc_start: 0.7638 (tmm) cc_final: 0.7412 (tmm) REVERT: D 741 ASN cc_start: 0.8945 (m-40) cc_final: 0.8439 (t0) REVERT: D 895 TRP cc_start: 0.7872 (m-90) cc_final: 0.6515 (p-90) REVERT: D 965 SER cc_start: 0.7795 (m) cc_final: 0.7141 (p) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2816 time to fit residues: 149.2887 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 : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 106 optimal weight: 0.0870 chunk 51 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.117766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102607 restraints weight = 77145.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102063 restraints weight = 76140.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102774 restraints weight = 61246.655| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22868 Z= 0.180 Angle : 0.565 7.654 31404 Z= 0.298 Chirality : 0.040 0.158 3868 Planarity : 0.004 0.063 3940 Dihedral : 4.419 21.053 3412 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2952 helix: 1.57 (0.11), residues: 2260 sheet: -2.50 (0.50), residues: 104 loop : -1.34 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 993 HIS 0.004 0.001 HIS A 844 PHE 0.023 0.002 PHE A 629 TYR 0.032 0.001 TYR D 772 ARG 0.004 0.000 ARG C 278 Details of bonding type rmsd link_TRANS : bond 0.00059 ( 4) link_TRANS : angle 0.11319 ( 12) hydrogen bonds : bond 0.03559 ( 1728) hydrogen bonds : angle 4.04455 ( 5172) covalent geometry : bond 0.00399 (22864) covalent geometry : angle 0.56530 (31392) *********************** 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 304 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 2.675 Fit side-chains REVERT: A 525 TRP cc_start: 0.8088 (t60) cc_final: 0.7812 (t60) REVERT: A 601 MET cc_start: 0.7582 (tmm) cc_final: 0.7300 (tmm) REVERT: A 615 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 741 ASN cc_start: 0.8931 (m-40) cc_final: 0.8481 (t0) REVERT: A 772 TYR cc_start: 0.7663 (m-80) cc_final: 0.7273 (m-80) REVERT: A 895 TRP cc_start: 0.7977 (m-90) cc_final: 0.6549 (p-90) REVERT: A 965 SER cc_start: 0.7591 (m) cc_final: 0.7091 (p) REVERT: B 525 TRP cc_start: 0.8142 (t60) cc_final: 0.7791 (t60) REVERT: B 741 ASN cc_start: 0.8923 (m-40) cc_final: 0.8474 (t0) REVERT: B 772 TYR cc_start: 0.7660 (m-80) cc_final: 0.7397 (m-80) REVERT: B 895 TRP cc_start: 0.7946 (m-90) cc_final: 0.6520 (p-90) REVERT: B 965 SER cc_start: 0.7433 (m) cc_final: 0.6883 (p) REVERT: C 525 TRP cc_start: 0.8134 (t60) cc_final: 0.7792 (t60) REVERT: C 601 MET cc_start: 0.7604 (tmm) cc_final: 0.7382 (tmm) REVERT: C 741 ASN cc_start: 0.8919 (m-40) cc_final: 0.8474 (t0) REVERT: C 772 TYR cc_start: 0.7666 (m-80) cc_final: 0.7395 (m-80) REVERT: C 895 TRP cc_start: 0.7930 (m-90) cc_final: 0.6515 (p-90) REVERT: C 965 SER cc_start: 0.7439 (m) cc_final: 0.6862 (p) REVERT: D 525 TRP cc_start: 0.8123 (t60) cc_final: 0.7785 (t60) REVERT: D 601 MET cc_start: 0.7597 (tmm) cc_final: 0.7374 (tmm) REVERT: D 741 ASN cc_start: 0.8923 (m-40) cc_final: 0.8470 (t0) REVERT: D 895 TRP cc_start: 0.7944 (m-90) cc_final: 0.6524 (p-90) REVERT: D 965 SER cc_start: 0.7740 (m) cc_final: 0.7112 (p) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2593 time to fit residues: 137.4778 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 : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 233 optimal weight: 30.0000 chunk 107 optimal weight: 0.1980 chunk 239 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 300 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 = 0.117976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101385 restraints weight = 76842.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101894 restraints weight = 68049.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102599 restraints weight = 50382.735| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22868 Z= 0.163 Angle : 0.557 7.530 31404 Z= 0.293 Chirality : 0.040 0.187 3868 Planarity : 0.004 0.064 3940 Dihedral : 4.364 19.523 3412 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2952 helix: 1.61 (0.11), residues: 2264 sheet: -2.25 (0.52), residues: 84 loop : -1.58 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 993 HIS 0.005 0.001 HIS D 844 PHE 0.024 0.001 PHE A 629 TYR 0.013 0.001 TYR D 497 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd link_TRANS : bond 0.00065 ( 4) link_TRANS : angle 0.11136 ( 12) hydrogen bonds : bond 0.03474 ( 1728) hydrogen bonds : angle 3.97226 ( 5172) covalent geometry : bond 0.00368 (22864) covalent geometry : angle 0.55724 (31392) *********************** 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 318 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 2.744 Fit side-chains REVERT: A 525 TRP cc_start: 0.8165 (t60) cc_final: 0.7857 (t60) REVERT: A 601 MET cc_start: 0.7642 (tmm) cc_final: 0.7309 (tmm) REVERT: A 615 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 741 ASN cc_start: 0.8920 (m-40) cc_final: 0.8477 (t0) REVERT: A 772 TYR cc_start: 0.7582 (m-80) cc_final: 0.7165 (m-80) REVERT: A 895 TRP cc_start: 0.8042 (m-90) cc_final: 0.6581 (p-90) REVERT: A 965 SER cc_start: 0.7484 (m) cc_final: 0.6989 (p) REVERT: B 525 TRP cc_start: 0.8146 (t60) cc_final: 0.7766 (t60) REVERT: B 741 ASN cc_start: 0.8911 (m-40) cc_final: 0.8466 (t0) REVERT: B 772 TYR cc_start: 0.7670 (m-80) cc_final: 0.7349 (m-80) REVERT: B 895 TRP cc_start: 0.7929 (m-90) cc_final: 0.6511 (p-90) REVERT: B 965 SER cc_start: 0.7344 (m) cc_final: 0.6816 (p) REVERT: C 525 TRP cc_start: 0.8157 (t60) cc_final: 0.7790 (t60) REVERT: C 601 MET cc_start: 0.7569 (tmm) cc_final: 0.7282 (tmm) REVERT: C 741 ASN cc_start: 0.8905 (m-40) cc_final: 0.8462 (t0) REVERT: C 772 TYR cc_start: 0.7671 (m-80) cc_final: 0.7343 (m-80) REVERT: C 895 TRP cc_start: 0.7918 (m-90) cc_final: 0.6514 (p-90) REVERT: C 965 SER cc_start: 0.7736 (m) cc_final: 0.7202 (p) REVERT: D 525 TRP cc_start: 0.8125 (t60) cc_final: 0.7785 (t60) REVERT: D 601 MET cc_start: 0.7569 (tmm) cc_final: 0.7285 (tmm) REVERT: D 741 ASN cc_start: 0.8909 (m-40) cc_final: 0.8456 (t0) REVERT: D 895 TRP cc_start: 0.7929 (m-90) cc_final: 0.6512 (p-90) REVERT: D 965 SER cc_start: 0.7723 (m) cc_final: 0.7100 (p) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2617 time to fit residues: 143.6314 Evaluate side-chains 244 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 34 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.119510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104650 restraints weight = 77338.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104673 restraints weight = 73084.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105382 restraints weight = 54706.339| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22868 Z= 0.122 Angle : 0.531 6.991 31404 Z= 0.276 Chirality : 0.039 0.176 3868 Planarity : 0.004 0.064 3940 Dihedral : 4.253 20.684 3412 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.16), residues: 2952 helix: 1.78 (0.11), residues: 2264 sheet: -2.36 (0.51), residues: 84 loop : -1.59 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 993 HIS 0.006 0.001 HIS C 844 PHE 0.023 0.001 PHE C 838 TYR 0.022 0.001 TYR D 772 ARG 0.003 0.000 ARG A 532 Details of bonding type rmsd link_TRANS : bond 0.00041 ( 4) link_TRANS : angle 0.14336 ( 12) hydrogen bonds : bond 0.03226 ( 1728) hydrogen bonds : angle 3.81336 ( 5172) covalent geometry : bond 0.00275 (22864) covalent geometry : angle 0.53092 (31392) ********************** 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 314 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 2.320 Fit side-chains REVERT: A 525 TRP cc_start: 0.8086 (t60) cc_final: 0.7779 (t60) REVERT: A 601 MET cc_start: 0.7622 (tmm) cc_final: 0.7262 (tmm) REVERT: A 615 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 741 ASN cc_start: 0.8919 (m-40) cc_final: 0.8428 (t0) REVERT: A 772 TYR cc_start: 0.7477 (m-80) cc_final: 0.7174 (m-80) REVERT: A 965 SER cc_start: 0.7295 (m) cc_final: 0.6891 (p) REVERT: B 525 TRP cc_start: 0.8042 (t60) cc_final: 0.7704 (t60) REVERT: B 741 ASN cc_start: 0.8905 (m-40) cc_final: 0.8429 (t0) REVERT: B 772 TYR cc_start: 0.7564 (m-80) cc_final: 0.7348 (m-80) REVERT: B 895 TRP cc_start: 0.7903 (m-90) cc_final: 0.6588 (p-90) REVERT: B 965 SER cc_start: 0.7160 (m) cc_final: 0.6722 (p) REVERT: C 525 TRP cc_start: 0.8053 (t60) cc_final: 0.7715 (t60) REVERT: C 601 MET cc_start: 0.7509 (tmm) cc_final: 0.7277 (tmm) REVERT: C 741 ASN cc_start: 0.8903 (m-40) cc_final: 0.8426 (t0) REVERT: C 772 TYR cc_start: 0.7553 (m-80) cc_final: 0.7348 (m-80) REVERT: C 895 TRP cc_start: 0.7908 (m-90) cc_final: 0.6585 (p-90) REVERT: C 965 SER cc_start: 0.7633 (m) cc_final: 0.7155 (p) REVERT: D 525 TRP cc_start: 0.8036 (t60) cc_final: 0.7706 (t60) REVERT: D 601 MET cc_start: 0.7518 (tmm) cc_final: 0.7280 (tmm) REVERT: D 741 ASN cc_start: 0.8911 (m-40) cc_final: 0.8423 (t0) REVERT: D 895 TRP cc_start: 0.7900 (m-90) cc_final: 0.6585 (p-90) REVERT: D 965 SER cc_start: 0.7530 (m) cc_final: 0.6897 (p) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2482 time to fit residues: 135.2671 Evaluate side-chains 258 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 122 optimal weight: 0.9990 chunk 273 optimal weight: 0.0020 chunk 228 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3794 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.120195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104681 restraints weight = 76515.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104649 restraints weight = 71577.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105139 restraints weight = 57139.573| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22868 Z= 0.116 Angle : 0.516 6.775 31404 Z= 0.268 Chirality : 0.039 0.170 3868 Planarity : 0.004 0.063 3940 Dihedral : 4.174 22.708 3412 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2952 helix: 1.88 (0.11), residues: 2264 sheet: -2.57 (0.46), residues: 92 loop : -1.60 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B 993 HIS 0.006 0.001 HIS C 844 PHE 0.036 0.002 PHE A 776 TYR 0.011 0.001 TYR B 497 ARG 0.002 0.000 ARG A 532 Details of bonding type rmsd link_TRANS : bond 0.00023 ( 4) link_TRANS : angle 0.14289 ( 12) hydrogen bonds : bond 0.03108 ( 1728) hydrogen bonds : angle 3.71111 ( 5172) covalent geometry : bond 0.00256 (22864) covalent geometry : angle 0.51568 (31392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5985.45 seconds wall clock time: 104 minutes 16.94 seconds (6256.94 seconds total)