Starting phenix.real_space_refine (version: dev) on Wed Dec 14 20:39:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/12_2022/6bpq_7127_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/12_2022/6bpq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/12_2022/6bpq_7127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/12_2022/6bpq_7127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/12_2022/6bpq_7127_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/12_2022/6bpq_7127_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 22404 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 5601 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 360} Link IDs: {'PTRANS': 19, 'TRANS': 815} Chain breaks: 18 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1205 Unresolved non-hydrogen angles: 1537 Unresolved non-hydrogen dihedrals: 922 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 16, 'ASN:plan1': 22, 'TYR:plan': 5, 'UNK:plan-1': 67, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 23, 'PHE:plan': 8, 'GLU:plan': 44, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 672 Chain: "B" Number of atoms: 5601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 5601 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 360} Link IDs: {'PTRANS': 19, 'TRANS': 815} Chain breaks: 18 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1205 Unresolved non-hydrogen angles: 1537 Unresolved non-hydrogen dihedrals: 922 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 16, 'ASN:plan1': 22, 'TYR:plan': 5, 'UNK:plan-1': 67, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 23, 'PHE:plan': 8, 'GLU:plan': 44, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 672 Chain: "C" Number of atoms: 5601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 5601 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 360} Link IDs: {'PTRANS': 19, 'TRANS': 815} Chain breaks: 18 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1205 Unresolved non-hydrogen angles: 1537 Unresolved non-hydrogen dihedrals: 922 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 16, 'ASN:plan1': 22, 'TYR:plan': 5, 'UNK:plan-1': 67, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 23, 'PHE:plan': 8, 'GLU:plan': 44, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 672 Chain: "D" Number of atoms: 5601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 5601 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 360} Link IDs: {'PTRANS': 19, 'TRANS': 815} Chain breaks: 18 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1205 Unresolved non-hydrogen angles: 1537 Unresolved non-hydrogen dihedrals: 922 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 16, 'ASN:plan1': 22, 'TYR:plan': 5, 'UNK:plan-1': 67, 'TRP:plan': 2, 'HIS:plan': 2, 'ARG:plan': 23, 'PHE:plan': 8, 'GLU:plan': 44, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 672 Time building chain proxies: 12.78, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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 Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 3.7 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: 1.47 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: 8.27 Time building geometry restraints manager: 10.29 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: 6953 1.34 - 1.46: 4544 1.46 - 1.57: 11267 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 22868 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 22863 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.60: 285 105.60 - 112.71: 12373 112.71 - 119.83: 7315 119.83 - 126.94: 11121 126.94 - 134.05: 310 Bond angle restraints: 31404 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 31399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 12244 14.78 - 29.56: 636 29.56 - 44.34: 84 44.34 - 59.13: 12 59.13 - 73.91: 8 Dihedral angle restraints: 12984 sinusoidal: 3172 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 12981 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 2.440 nonbonded pdb=" O LEU B 592 " pdb=" OG SER B 595 " model vdw 2.338 2.440 nonbonded pdb=" O LEU C 592 " pdb=" OG SER C 595 " model vdw 2.338 2.440 nonbonded pdb=" O LEU A 592 " pdb=" OG SER A 595 " model vdw 2.338 2.440 nonbonded pdb=" O SER B 823 " pdb=" OG SER B 826 " model vdw 2.346 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 0.780 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: 5.570 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.180 Process input model: 59.110 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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= 0.434 Angle : 0.918 11.361 31404 Z= 0.503 Chirality : 0.053 0.323 3868 Planarity : 0.007 0.071 3944 Dihedral : 9.829 73.908 6528 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 % 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: -3.30 (0.12), residues: 2952 helix: -1.92 (0.08), residues: 2132 sheet: -1.07 (0.59), residues: 80 loop : -2.51 (0.19), residues: 740 *********************** 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 fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 2.682 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.2967 time to fit residues: 238.8669 Evaluate side-chains 244 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 301 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 HIS A 419 ASN A 681 GLN B 389 HIS B 419 ASN B 681 GLN C 389 HIS C 419 ASN C 681 GLN D 389 HIS D 419 ASN D 681 GLN ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 22868 Z= 0.434 Angle : 0.736 7.364 31404 Z= 0.394 Chirality : 0.044 0.171 3868 Planarity : 0.006 0.065 3944 Dihedral : 5.388 24.860 3416 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.88 (0.15), residues: 2952 helix: -0.03 (0.10), residues: 2224 sheet: -2.18 (0.44), residues: 120 loop : -1.85 (0.24), residues: 608 *********************** 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 339 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.634 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2827 time to fit residues: 158.2976 Evaluate side-chains 241 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 250 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 302 optimal weight: 30.0000 chunk 326 optimal weight: 20.0000 chunk 268 optimal weight: 0.0870 chunk 299 optimal weight: 5.9990 chunk 102 optimal weight: 0.0570 chunk 242 optimal weight: 0.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 22868 Z= 0.187 Angle : 0.525 5.775 31404 Z= 0.279 Chirality : 0.039 0.163 3868 Planarity : 0.004 0.066 3944 Dihedral : 4.721 21.821 3416 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.15), residues: 2952 helix: 0.96 (0.11), residues: 2268 sheet: -1.70 (0.44), residues: 120 loop : -1.75 (0.26), residues: 564 *********************** 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 356 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 2.545 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2505 time to fit residues: 152.7082 Evaluate side-chains 236 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 320 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN B 419 ASN C 419 ASN D 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 22868 Z= 0.432 Angle : 0.724 9.553 31404 Z= 0.379 Chirality : 0.044 0.168 3868 Planarity : 0.005 0.063 3944 Dihedral : 5.092 24.726 3416 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.16), residues: 2952 helix: 0.90 (0.11), residues: 2240 sheet: -2.26 (0.46), residues: 80 loop : -1.69 (0.25), residues: 632 *********************** 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 280 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.612 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2607 time to fit residues: 126.7726 Evaluate side-chains 218 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.577 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 238 optimal weight: 0.0060 chunk 132 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 22868 Z= 0.152 Angle : 0.501 6.288 31404 Z= 0.267 Chirality : 0.039 0.158 3868 Planarity : 0.004 0.065 3944 Dihedral : 4.486 22.091 3416 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.16), residues: 2952 helix: 1.55 (0.11), residues: 2264 sheet: -1.76 (0.41), residues: 140 loop : -1.52 (0.28), residues: 548 *********************** 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 324 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.551 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2572 time to fit residues: 143.7668 Evaluate side-chains 220 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 106 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22868 Z= 0.189 Angle : 0.527 6.563 31404 Z= 0.275 Chirality : 0.039 0.155 3868 Planarity : 0.004 0.066 3944 Dihedral : 4.325 19.450 3416 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.16), residues: 2952 helix: 1.71 (0.11), residues: 2268 sheet: -1.86 (0.41), residues: 148 loop : -1.34 (0.29), residues: 536 *********************** 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 327 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2645 time to fit residues: 146.8931 Evaluate side-chains 241 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 270 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 22868 Z= 0.324 Angle : 0.630 7.601 31404 Z= 0.330 Chirality : 0.042 0.165 3868 Planarity : 0.004 0.065 3944 Dihedral : 4.616 21.544 3416 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.16), residues: 2952 helix: 1.52 (0.11), residues: 2268 sheet: -2.19 (0.40), residues: 148 loop : -1.42 (0.29), residues: 536 *********************** 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 293 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.618 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2632 time to fit residues: 132.7000 Evaluate side-chains 228 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 203 optimal weight: 0.1980 chunk 218 optimal weight: 0.0770 chunk 158 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 overall best weight: 2.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22868 Z= 0.213 Angle : 0.558 8.137 31404 Z= 0.290 Chirality : 0.040 0.159 3868 Planarity : 0.004 0.066 3944 Dihedral : 4.382 20.023 3416 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.16), residues: 2952 helix: 1.71 (0.11), residues: 2268 sheet: -1.82 (0.41), residues: 148 loop : -1.43 (0.29), residues: 536 *********************** 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 298 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.573 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2573 time to fit residues: 132.1252 Evaluate side-chains 227 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.296 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 282 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 22868 Z= 0.329 Angle : 0.643 7.889 31404 Z= 0.337 Chirality : 0.043 0.189 3868 Planarity : 0.004 0.066 3944 Dihedral : 4.646 20.903 3416 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.16), residues: 2952 helix: 1.49 (0.11), residues: 2268 sheet: -1.84 (0.46), residues: 104 loop : -1.65 (0.27), residues: 580 *********************** 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 277 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.767 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2644 time to fit residues: 126.8888 Evaluate side-chains 214 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 10.0000 chunk 315 optimal weight: 1.9990 chunk 192 optimal weight: 0.4980 chunk 149 optimal weight: 7.9990 chunk 219 optimal weight: 40.0000 chunk 330 optimal weight: 20.0000 chunk 304 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 22868 Z= 0.317 Angle : 0.628 7.295 31404 Z= 0.330 Chirality : 0.043 0.174 3868 Planarity : 0.004 0.067 3944 Dihedral : 4.642 20.956 3416 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.16), residues: 2952 helix: 1.47 (0.11), residues: 2268 sheet: -1.92 (0.45), residues: 104 loop : -1.70 (0.27), residues: 580 ********************** 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 269 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 2.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2612 time to fit residues: 121.5331 Evaluate side-chains 216 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 263 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.120517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103540 restraints weight = 76487.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104338 restraints weight = 60327.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104767 restraints weight = 45099.454| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.083 22868 Z= 0.156 Angle : 0.535 8.412 31404 Z= 0.278 Chirality : 0.039 0.167 3868 Planarity : 0.004 0.067 3944 Dihedral : 4.275 20.524 3416 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.16), residues: 2952 helix: 1.85 (0.11), residues: 2264 sheet: -1.93 (0.39), residues: 160 loop : -1.54 (0.28), residues: 528 =============================================================================== Job complete usr+sys time: 3517.32 seconds wall clock time: 64 minutes 55.29 seconds (3895.29 seconds total)