Starting phenix.real_space_refine on Mon Mar 18 23:23:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/03_2024/6bpq_7127_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/03_2024/6bpq_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_7127/03_2024/6bpq_7127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/03_2024/6bpq_7127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/03_2024/6bpq_7127_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpq_7127/03_2024/6bpq_7127_neut.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.96, per 1000 atoms: 0.53 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: 8.84 Conformation dependent library (CDL) restraints added in 4.0 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: 2.44 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: 7.85 Time building geometry restraints manager: 9.55 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 4.900 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 57.180 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.110 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.930 ------------------------------------------------------------------------------- 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= 0.434 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 % 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: -3.30 (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 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 *********************** 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 : 2.546 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: 0.2825 time to fit residues: 225.3593 Evaluate side-chains 255 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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: 5.9990 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: 5.5990 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 22868 Z= 0.447 Angle : 0.742 7.665 31404 Z= 0.396 Chirality : 0.044 0.168 3868 Planarity : 0.006 0.065 3944 Dihedral : 5.423 25.221 3416 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % 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: -0.92 (0.15), residues: 2952 helix: -0.06 (0.10), residues: 2224 sheet: -2.17 (0.44), residues: 120 loop : -1.86 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 993 HIS 0.009 0.002 HIS B 389 PHE 0.017 0.002 PHE A 629 TYR 0.011 0.002 TYR A 295 ARG 0.005 0.001 ARG D 532 *********************** 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 341 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.348 Fit side-chains REVERT: A 525 TRP cc_start: 0.8279 (t60) cc_final: 0.7920 (t60) REVERT: A 615 GLU cc_start: 0.8319 (tt0) cc_final: 0.7969 (tm-30) REVERT: A 752 PHE cc_start: 0.8782 (t80) cc_final: 0.8196 (t80) REVERT: A 772 TYR cc_start: 0.8060 (m-80) cc_final: 0.7679 (m-80) REVERT: A 835 TYR cc_start: 0.8950 (t80) cc_final: 0.8571 (t80) REVERT: A 844 HIS cc_start: 0.9180 (t-90) cc_final: 0.8962 (t-90) REVERT: B 170 TYR cc_start: 0.8532 (t80) cc_final: 0.8305 (t80) REVERT: B 525 TRP cc_start: 0.8367 (t60) cc_final: 0.7962 (t60) REVERT: B 615 GLU cc_start: 0.8282 (tt0) cc_final: 0.8081 (tm-30) REVERT: B 741 ASN cc_start: 0.8846 (m-40) cc_final: 0.8605 (t0) REVERT: B 752 PHE cc_start: 0.8822 (t80) cc_final: 0.8127 (t80) REVERT: B 772 TYR cc_start: 0.7956 (m-80) cc_final: 0.7573 (m-80) REVERT: B 835 TYR cc_start: 0.8892 (t80) cc_final: 0.8441 (t80) REVERT: B 844 HIS cc_start: 0.9062 (t70) cc_final: 0.8834 (t-90) REVERT: B 895 TRP cc_start: 0.8020 (m-90) cc_final: 0.6157 (p-90) REVERT: C 170 TYR cc_start: 0.8536 (t80) cc_final: 0.8308 (t80) REVERT: C 525 TRP cc_start: 0.8369 (t60) cc_final: 0.7963 (t60) REVERT: C 741 ASN cc_start: 0.8840 (m-40) cc_final: 0.8602 (t0) REVERT: C 752 PHE cc_start: 0.8819 (t80) cc_final: 0.8129 (t80) REVERT: C 772 TYR cc_start: 0.7959 (m-80) cc_final: 0.7577 (m-80) REVERT: C 835 TYR cc_start: 0.8890 (t80) cc_final: 0.8439 (t80) REVERT: C 844 HIS cc_start: 0.9062 (t70) cc_final: 0.8836 (t-90) REVERT: C 895 TRP cc_start: 0.8017 (m-90) cc_final: 0.6155 (p-90) REVERT: D 170 TYR cc_start: 0.8536 (t80) cc_final: 0.8308 (t80) REVERT: D 525 TRP cc_start: 0.8375 (t60) cc_final: 0.7961 (t60) REVERT: D 741 ASN cc_start: 0.8840 (m-40) cc_final: 0.8604 (t0) REVERT: D 752 PHE cc_start: 0.8819 (t80) cc_final: 0.8129 (t80) REVERT: D 772 TYR cc_start: 0.7957 (m-80) cc_final: 0.7574 (m-80) REVERT: D 835 TYR cc_start: 0.8896 (t80) cc_final: 0.8440 (t80) REVERT: D 844 HIS cc_start: 0.9063 (t70) cc_final: 0.8836 (t-90) REVERT: D 895 TRP cc_start: 0.8019 (m-90) cc_final: 0.6158 (p-90) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2818 time to fit residues: 158.7832 Evaluate side-chains 262 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 20.0000 chunk 302 optimal weight: 30.0000 chunk 326 optimal weight: 20.0000 chunk 268 optimal weight: 0.7980 chunk 299 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 242 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.2169 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= 0.211 Angle : 0.536 5.918 31404 Z= 0.287 Chirality : 0.039 0.165 3868 Planarity : 0.004 0.066 3944 Dihedral : 4.748 21.817 3416 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.15), residues: 2952 helix: 0.97 (0.11), residues: 2244 sheet: -1.75 (0.45), residues: 120 loop : -1.71 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 993 HIS 0.003 0.001 HIS B 844 PHE 0.019 0.002 PHE A 629 TYR 0.012 0.001 TYR B 772 ARG 0.005 0.001 ARG C 532 *********************** 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 357 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.487 Fit side-chains REVERT: A 525 TRP cc_start: 0.8223 (t60) cc_final: 0.7878 (t60) REVERT: A 596 LYS cc_start: 0.9038 (tppt) cc_final: 0.8791 (tppt) REVERT: A 772 TYR cc_start: 0.7777 (m-80) cc_final: 0.7267 (m-10) REVERT: A 965 SER cc_start: 0.7685 (m) cc_final: 0.7037 (p) REVERT: A 971 VAL cc_start: 0.8939 (t) cc_final: 0.8688 (p) REVERT: B 525 TRP cc_start: 0.8284 (t60) cc_final: 0.7892 (t60) REVERT: B 596 LYS cc_start: 0.9066 (tppt) cc_final: 0.8796 (tppt) REVERT: B 772 TYR cc_start: 0.7857 (m-80) cc_final: 0.7318 (m-80) REVERT: B 776 PHE cc_start: 0.7606 (m-80) cc_final: 0.7360 (m-80) REVERT: B 844 HIS cc_start: 0.8986 (t70) cc_final: 0.8779 (t-90) REVERT: B 895 TRP cc_start: 0.8049 (m-90) cc_final: 0.6314 (p-90) REVERT: B 955 THR cc_start: 0.8842 (t) cc_final: 0.8577 (t) REVERT: B 965 SER cc_start: 0.7647 (m) cc_final: 0.7005 (p) REVERT: B 971 VAL cc_start: 0.8967 (t) cc_final: 0.8728 (p) REVERT: C 525 TRP cc_start: 0.8248 (t60) cc_final: 0.7849 (t60) REVERT: C 596 LYS cc_start: 0.9070 (tppt) cc_final: 0.8788 (tppt) REVERT: C 601 MET cc_start: 0.7830 (tmm) cc_final: 0.7629 (tmm) REVERT: C 615 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7520 (tm-30) REVERT: C 772 TYR cc_start: 0.7852 (m-80) cc_final: 0.7322 (m-80) REVERT: C 776 PHE cc_start: 0.7603 (m-80) cc_final: 0.7360 (m-80) REVERT: C 844 HIS cc_start: 0.8987 (t70) cc_final: 0.8778 (t-90) REVERT: C 895 TRP cc_start: 0.8047 (m-90) cc_final: 0.6310 (p-90) REVERT: C 955 THR cc_start: 0.8844 (t) cc_final: 0.8585 (t) REVERT: C 965 SER cc_start: 0.7642 (m) cc_final: 0.6994 (p) REVERT: C 971 VAL cc_start: 0.8976 (t) cc_final: 0.8733 (p) REVERT: D 525 TRP cc_start: 0.8292 (t60) cc_final: 0.7904 (t60) REVERT: D 596 LYS cc_start: 0.9068 (tppt) cc_final: 0.8793 (tppt) REVERT: D 615 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7517 (tm-30) REVERT: D 772 TYR cc_start: 0.7855 (m-80) cc_final: 0.7318 (m-80) REVERT: D 776 PHE cc_start: 0.7605 (m-80) cc_final: 0.7359 (m-80) REVERT: D 844 HIS cc_start: 0.8984 (t70) cc_final: 0.8778 (t-90) REVERT: D 895 TRP cc_start: 0.8051 (m-90) cc_final: 0.6313 (p-90) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2684 time to fit residues: 161.0803 Evaluate side-chains 248 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.413 ------------------------------------------------------------------------------- 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: 0.8980 chunk 227 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 320 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 287 optimal weight: 4.9990 chunk 86 optimal weight: 0.0070 overall best weight: 2.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22868 Z= 0.217 Angle : 0.538 6.484 31404 Z= 0.283 Chirality : 0.039 0.158 3868 Planarity : 0.004 0.064 3944 Dihedral : 4.503 21.200 3416 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 1.05 (0.16), residues: 2952 helix: 1.41 (0.11), residues: 2264 sheet: -1.83 (0.45), residues: 120 loop : -1.52 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 993 HIS 0.003 0.001 HIS D 844 PHE 0.018 0.002 PHE D 871 TYR 0.010 0.001 TYR B 772 ARG 0.009 0.001 ARG B 278 *********************** 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 325 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.536 Fit side-chains REVERT: A 358 LEU cc_start: 0.7821 (mt) cc_final: 0.7543 (tt) REVERT: A 525 TRP cc_start: 0.8279 (t60) cc_final: 0.7903 (t60) REVERT: A 615 GLU cc_start: 0.8341 (tt0) cc_final: 0.8039 (tm-30) REVERT: A 772 TYR cc_start: 0.7820 (m-80) cc_final: 0.7461 (m-80) REVERT: A 965 SER cc_start: 0.7581 (m) cc_final: 0.6961 (p) REVERT: A 971 VAL cc_start: 0.8952 (t) cc_final: 0.8723 (p) REVERT: B 358 LEU cc_start: 0.7858 (mt) cc_final: 0.7581 (tt) REVERT: B 525 TRP cc_start: 0.8287 (t60) cc_final: 0.7895 (t60) REVERT: B 615 GLU cc_start: 0.8336 (tt0) cc_final: 0.8038 (tm-30) REVERT: B 772 TYR cc_start: 0.7894 (m-80) cc_final: 0.7445 (m-80) REVERT: B 844 HIS cc_start: 0.8962 (t70) cc_final: 0.8759 (t-90) REVERT: B 895 TRP cc_start: 0.8053 (m-90) cc_final: 0.6384 (p-90) REVERT: B 955 THR cc_start: 0.8796 (t) cc_final: 0.8591 (t) REVERT: B 965 SER cc_start: 0.7475 (m) cc_final: 0.6870 (p) REVERT: C 358 LEU cc_start: 0.7855 (mt) cc_final: 0.7576 (tt) REVERT: C 525 TRP cc_start: 0.8291 (t60) cc_final: 0.7896 (t60) REVERT: C 601 MET cc_start: 0.7867 (tmm) cc_final: 0.7597 (tmm) REVERT: C 615 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 772 TYR cc_start: 0.7897 (m-80) cc_final: 0.7448 (m-80) REVERT: C 844 HIS cc_start: 0.8966 (t70) cc_final: 0.8764 (t-90) REVERT: C 895 TRP cc_start: 0.8052 (m-90) cc_final: 0.6383 (p-90) REVERT: C 955 THR cc_start: 0.8805 (t) cc_final: 0.8600 (t) REVERT: C 965 SER cc_start: 0.7466 (m) cc_final: 0.6869 (p) REVERT: D 358 LEU cc_start: 0.7857 (mt) cc_final: 0.7579 (tt) REVERT: D 525 TRP cc_start: 0.8300 (t60) cc_final: 0.7902 (t60) REVERT: D 615 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 772 TYR cc_start: 0.7852 (m-80) cc_final: 0.7395 (m-80) REVERT: D 895 TRP cc_start: 0.8057 (m-90) cc_final: 0.6381 (p-90) REVERT: D 965 SER cc_start: 0.7459 (m) cc_final: 0.6779 (p) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2566 time to fit residues: 144.0718 Evaluate side-chains 247 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.517 ------------------------------------------------------------------------------- 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: 10.0000 chunk 182 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 238 optimal weight: 0.0770 chunk 132 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7801 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22868 Z= 0.194 Angle : 0.503 5.745 31404 Z= 0.267 Chirality : 0.039 0.161 3868 Planarity : 0.004 0.065 3944 Dihedral : 4.360 20.715 3416 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.16), residues: 2952 helix: 1.67 (0.11), residues: 2264 sheet: -2.21 (0.40), residues: 148 loop : -1.41 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 993 HIS 0.003 0.001 HIS D 844 PHE 0.018 0.001 PHE D 838 TYR 0.010 0.001 TYR B 772 ARG 0.006 0.001 ARG C 278 *********************** 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 325 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.579 Fit side-chains REVERT: A 358 LEU cc_start: 0.7903 (mt) cc_final: 0.7662 (tt) REVERT: A 525 TRP cc_start: 0.8257 (t60) cc_final: 0.7886 (t60) REVERT: A 615 GLU cc_start: 0.8329 (tt0) cc_final: 0.8030 (tm-30) REVERT: A 772 TYR cc_start: 0.7846 (m-80) cc_final: 0.7514 (m-80) REVERT: A 965 SER cc_start: 0.7443 (m) cc_final: 0.6802 (p) REVERT: B 358 LEU cc_start: 0.7898 (mt) cc_final: 0.7658 (tt) REVERT: B 525 TRP cc_start: 0.8222 (t60) cc_final: 0.7812 (t60) REVERT: B 615 GLU cc_start: 0.8343 (tt0) cc_final: 0.8026 (tm-30) REVERT: B 772 TYR cc_start: 0.7818 (m-80) cc_final: 0.7345 (m-80) REVERT: B 895 TRP cc_start: 0.8091 (m-90) cc_final: 0.6572 (p-90) REVERT: B 965 SER cc_start: 0.7241 (m) cc_final: 0.6631 (p) REVERT: C 358 LEU cc_start: 0.7892 (mt) cc_final: 0.7657 (tt) REVERT: C 525 TRP cc_start: 0.8226 (t60) cc_final: 0.7809 (t60) REVERT: C 601 MET cc_start: 0.7811 (tmm) cc_final: 0.7463 (tmm) REVERT: C 615 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7600 (tm-30) REVERT: C 772 TYR cc_start: 0.7820 (m-80) cc_final: 0.7351 (m-80) REVERT: C 844 HIS cc_start: 0.8926 (t70) cc_final: 0.8697 (t-90) REVERT: C 895 TRP cc_start: 0.8088 (m-90) cc_final: 0.6569 (p-90) REVERT: C 965 SER cc_start: 0.7217 (m) cc_final: 0.6637 (p) REVERT: D 358 LEU cc_start: 0.7889 (mt) cc_final: 0.7655 (tt) REVERT: D 525 TRP cc_start: 0.8235 (t60) cc_final: 0.7815 (t60) REVERT: D 615 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 772 TYR cc_start: 0.7819 (m-80) cc_final: 0.7347 (m-80) REVERT: D 776 PHE cc_start: 0.7800 (m-80) cc_final: 0.7600 (m-80) REVERT: D 895 TRP cc_start: 0.8097 (m-90) cc_final: 0.6574 (p-90) REVERT: D 965 SER cc_start: 0.7075 (m) cc_final: 0.6531 (p) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2565 time to fit residues: 143.4856 Evaluate side-chains 248 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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: 4.9990 chunk 288 optimal weight: 0.0070 chunk 63 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 0.0270 chunk 168 optimal weight: 10.0000 overall best weight: 1.6060 ------------------------------------------------------------------------------- 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** ** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** 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: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22868 Z= 0.172 Angle : 0.485 5.861 31404 Z= 0.258 Chirality : 0.038 0.156 3868 Planarity : 0.004 0.063 3944 Dihedral : 4.190 20.506 3416 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 1.67 (0.16), residues: 2952 helix: 1.87 (0.11), residues: 2264 sheet: -1.69 (0.46), residues: 128 loop : -1.34 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 993 HIS 0.004 0.001 HIS D 844 PHE 0.021 0.001 PHE A 629 TYR 0.010 0.001 TYR C 772 ARG 0.003 0.000 ARG A 532 *********************** 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 337 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.418 Fit side-chains REVERT: A 358 LEU cc_start: 0.7961 (mt) cc_final: 0.7732 (tt) REVERT: A 525 TRP cc_start: 0.8227 (t60) cc_final: 0.7849 (t60) REVERT: A 615 GLU cc_start: 0.8328 (tt0) cc_final: 0.8026 (tm-30) REVERT: A 772 TYR cc_start: 0.7791 (m-80) cc_final: 0.7474 (m-80) REVERT: A 965 SER cc_start: 0.7218 (m) cc_final: 0.6650 (p) REVERT: B 358 LEU cc_start: 0.7823 (mt) cc_final: 0.7622 (tt) REVERT: B 525 TRP cc_start: 0.8169 (t60) cc_final: 0.7762 (t60) REVERT: B 601 MET cc_start: 0.7765 (tmm) cc_final: 0.7421 (tmm) REVERT: B 895 TRP cc_start: 0.8066 (m-90) cc_final: 0.6580 (p-90) REVERT: B 965 SER cc_start: 0.7162 (m) cc_final: 0.6385 (p) REVERT: C 525 TRP cc_start: 0.8181 (t60) cc_final: 0.7766 (t60) REVERT: C 615 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 772 TYR cc_start: 0.7879 (m-80) cc_final: 0.7487 (m-80) REVERT: C 895 TRP cc_start: 0.8063 (m-90) cc_final: 0.6578 (p-90) REVERT: C 965 SER cc_start: 0.7442 (m) cc_final: 0.6895 (p) REVERT: D 525 TRP cc_start: 0.8176 (t60) cc_final: 0.7771 (t60) REVERT: D 601 MET cc_start: 0.7806 (tmm) cc_final: 0.7562 (tmm) REVERT: D 615 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7593 (tm-30) REVERT: D 772 TYR cc_start: 0.7903 (m-80) cc_final: 0.7552 (m-80) REVERT: D 895 TRP cc_start: 0.8068 (m-90) cc_final: 0.6579 (p-90) REVERT: D 965 SER cc_start: 0.7146 (m) cc_final: 0.6775 (p) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2568 time to fit residues: 147.2965 Evaluate side-chains 257 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 7.9990 chunk 183 optimal weight: 0.0980 chunk 234 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22868 Z= 0.144 Angle : 0.476 6.619 31404 Z= 0.250 Chirality : 0.038 0.149 3868 Planarity : 0.004 0.063 3944 Dihedral : 4.045 19.522 3416 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.79 (0.16), residues: 2952 helix: 1.97 (0.11), residues: 2264 sheet: -1.82 (0.42), residues: 148 loop : -1.30 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 993 HIS 0.004 0.001 HIS D 844 PHE 0.023 0.001 PHE B 776 TYR 0.011 0.001 TYR C 772 ARG 0.004 0.000 ARG B 532 *********************** 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 349 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.596 Fit side-chains REVERT: A 525 TRP cc_start: 0.8209 (t60) cc_final: 0.7810 (t60) REVERT: A 601 MET cc_start: 0.7687 (tmm) cc_final: 0.7476 (tmm) REVERT: A 772 TYR cc_start: 0.7900 (m-80) cc_final: 0.7448 (m-80) REVERT: A 776 PHE cc_start: 0.7703 (m-80) cc_final: 0.7497 (m-80) REVERT: A 965 SER cc_start: 0.7411 (m) cc_final: 0.6892 (p) REVERT: B 525 TRP cc_start: 0.8183 (t60) cc_final: 0.7778 (t60) REVERT: B 895 TRP cc_start: 0.8049 (m-90) cc_final: 0.6600 (p-90) REVERT: B 965 SER cc_start: 0.7161 (m) cc_final: 0.6454 (p) REVERT: C 525 TRP cc_start: 0.8179 (t60) cc_final: 0.7791 (t60) REVERT: C 615 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 772 TYR cc_start: 0.7807 (m-80) cc_final: 0.7516 (m-80) REVERT: C 895 TRP cc_start: 0.8050 (m-90) cc_final: 0.6604 (p-90) REVERT: C 965 SER cc_start: 0.7340 (m) cc_final: 0.6839 (p) REVERT: D 525 TRP cc_start: 0.8193 (t60) cc_final: 0.7800 (t60) REVERT: D 601 MET cc_start: 0.7732 (tmm) cc_final: 0.7473 (tmm) REVERT: D 772 TYR cc_start: 0.7841 (m-80) cc_final: 0.7559 (m-80) REVERT: D 895 TRP cc_start: 0.8053 (m-90) cc_final: 0.6604 (p-90) REVERT: D 965 SER cc_start: 0.7120 (m) cc_final: 0.6718 (p) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2572 time to fit residues: 154.3011 Evaluate side-chains 259 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.410 ------------------------------------------------------------------------------- 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: 4.9990 chunk 127 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 251 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 419 ASN ** 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: 0.7824 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22868 Z= 0.250 Angle : 0.550 7.108 31404 Z= 0.287 Chirality : 0.040 0.160 3868 Planarity : 0.004 0.062 3944 Dihedral : 4.165 19.289 3416 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: 1.68 (0.16), residues: 2952 helix: 1.84 (0.11), residues: 2268 sheet: -1.72 (0.47), residues: 128 loop : -1.21 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 993 HIS 0.004 0.001 HIS C 844 PHE 0.023 0.001 PHE A 629 TYR 0.031 0.001 TYR B 772 ARG 0.003 0.000 ARG A 997 *********************** 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 326 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.987 Fit side-chains revert: symmetry clash REVERT: A 525 TRP cc_start: 0.8225 (t60) cc_final: 0.7845 (t60) REVERT: A 772 TYR cc_start: 0.7860 (m-80) cc_final: 0.7500 (m-80) REVERT: A 904 TYR cc_start: 0.6292 (m-10) cc_final: 0.5918 (m-80) REVERT: A 965 SER cc_start: 0.7475 (m) cc_final: 0.6947 (p) REVERT: B 525 TRP cc_start: 0.8187 (t60) cc_final: 0.7763 (t60) REVERT: B 895 TRP cc_start: 0.8053 (m-90) cc_final: 0.6581 (p-90) REVERT: B 904 TYR cc_start: 0.6293 (m-10) cc_final: 0.5947 (m-80) REVERT: B 965 SER cc_start: 0.7158 (m) cc_final: 0.6519 (p) REVERT: C 525 TRP cc_start: 0.8174 (t60) cc_final: 0.7753 (t60) REVERT: C 615 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 772 TYR cc_start: 0.7919 (m-80) cc_final: 0.7503 (m-80) REVERT: C 895 TRP cc_start: 0.8059 (m-90) cc_final: 0.6580 (p-90) REVERT: C 904 TYR cc_start: 0.6287 (m-10) cc_final: 0.5960 (m-80) REVERT: C 965 SER cc_start: 0.7187 (m) cc_final: 0.6561 (p) REVERT: D 525 TRP cc_start: 0.8194 (t60) cc_final: 0.7771 (t60) REVERT: D 772 TYR cc_start: 0.7888 (m-80) cc_final: 0.7597 (m-80) REVERT: D 895 TRP cc_start: 0.8064 (m-90) cc_final: 0.6584 (p-90) REVERT: D 904 TYR cc_start: 0.6292 (m-10) cc_final: 0.5958 (m-80) REVERT: D 965 SER cc_start: 0.7329 (m) cc_final: 0.6848 (p) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2430 time to fit residues: 137.7835 Evaluate side-chains 256 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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: 0.2980 chunk 306 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 282 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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** ** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22868 Z= 0.205 Angle : 0.521 6.785 31404 Z= 0.271 Chirality : 0.039 0.158 3868 Planarity : 0.004 0.062 3944 Dihedral : 4.082 19.567 3416 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.71 (0.16), residues: 2952 helix: 1.92 (0.11), residues: 2260 sheet: -1.85 (0.42), residues: 148 loop : -1.36 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A 993 HIS 0.005 0.001 HIS C 844 PHE 0.022 0.001 PHE A 629 TYR 0.010 0.001 TYR C 772 ARG 0.003 0.000 ARG D 997 *********************** 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 323 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.441 Fit side-chains revert: symmetry clash REVERT: A 525 TRP cc_start: 0.8207 (t60) cc_final: 0.7832 (t60) REVERT: A 615 GLU cc_start: 0.8250 (tt0) cc_final: 0.7986 (tm-30) REVERT: A 772 TYR cc_start: 0.7892 (m-80) cc_final: 0.7583 (m-80) REVERT: A 904 TYR cc_start: 0.6141 (m-10) cc_final: 0.5602 (m-80) REVERT: A 965 SER cc_start: 0.7461 (m) cc_final: 0.6954 (p) REVERT: B 525 TRP cc_start: 0.8159 (t60) cc_final: 0.7756 (t60) REVERT: B 615 GLU cc_start: 0.8292 (tt0) cc_final: 0.7977 (tm-30) REVERT: B 895 TRP cc_start: 0.8102 (m-90) cc_final: 0.6585 (p-90) REVERT: B 904 TYR cc_start: 0.6218 (m-10) cc_final: 0.5692 (m-80) REVERT: B 965 SER cc_start: 0.7058 (m) cc_final: 0.6482 (p) REVERT: C 525 TRP cc_start: 0.8150 (t60) cc_final: 0.7736 (t60) REVERT: C 615 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7718 (tm-30) REVERT: C 772 TYR cc_start: 0.7830 (m-80) cc_final: 0.7515 (m-80) REVERT: C 895 TRP cc_start: 0.8099 (m-90) cc_final: 0.6588 (p-90) REVERT: C 904 TYR cc_start: 0.6233 (m-10) cc_final: 0.5718 (m-80) REVERT: C 965 SER cc_start: 0.7202 (m) cc_final: 0.6582 (p) REVERT: D 525 TRP cc_start: 0.8187 (t60) cc_final: 0.7760 (t60) REVERT: D 772 TYR cc_start: 0.7862 (m-80) cc_final: 0.7597 (m-80) REVERT: D 895 TRP cc_start: 0.8108 (m-90) cc_final: 0.6586 (p-90) REVERT: D 904 TYR cc_start: 0.6230 (m-10) cc_final: 0.5708 (m-80) REVERT: D 965 SER cc_start: 0.7308 (m) cc_final: 0.6840 (p) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2481 time to fit residues: 138.7651 Evaluate side-chains 250 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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: 9.9990 chunk 315 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 219 optimal weight: 30.0000 chunk 330 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 203 optimal weight: 0.0070 chunk 161 optimal weight: 30.0000 overall best weight: 5.4006 ------------------------------------------------------------------------------- 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 419 ASN ** 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: 0.7911 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22868 Z= 0.421 Angle : 0.686 8.369 31404 Z= 0.362 Chirality : 0.045 0.168 3868 Planarity : 0.005 0.064 3944 Dihedral : 4.652 23.440 3416 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 1.01 (0.16), residues: 2952 helix: 1.40 (0.11), residues: 2264 sheet: -2.49 (0.41), residues: 128 loop : -1.42 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 993 HIS 0.004 0.001 HIS B 259 PHE 0.025 0.002 PHE A 629 TYR 0.027 0.002 TYR A 497 ARG 0.006 0.001 ARG B 997 ********************** 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 286 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.489 Fit side-chains revert: symmetry clash REVERT: A 525 TRP cc_start: 0.8206 (t60) cc_final: 0.7835 (t60) REVERT: A 895 TRP cc_start: 0.8183 (m-90) cc_final: 0.6590 (p-90) REVERT: A 904 TYR cc_start: 0.6148 (m-10) cc_final: 0.5731 (m-80) REVERT: A 965 SER cc_start: 0.7736 (m) cc_final: 0.7133 (p) REVERT: B 146 ILE cc_start: 0.7819 (tp) cc_final: 0.7398 (tp) REVERT: B 525 TRP cc_start: 0.8214 (t60) cc_final: 0.7822 (t60) REVERT: B 776 PHE cc_start: 0.7932 (m-80) cc_final: 0.7698 (m-80) REVERT: B 895 TRP cc_start: 0.8108 (m-90) cc_final: 0.6522 (p-90) REVERT: B 904 TYR cc_start: 0.6118 (m-10) cc_final: 0.5686 (m-80) REVERT: B 965 SER cc_start: 0.7386 (m) cc_final: 0.6863 (p) REVERT: C 525 TRP cc_start: 0.8198 (t60) cc_final: 0.7812 (t60) REVERT: C 615 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 895 TRP cc_start: 0.8105 (m-90) cc_final: 0.6521 (p-90) REVERT: C 904 TYR cc_start: 0.6131 (m-10) cc_final: 0.5718 (m-80) REVERT: C 965 SER cc_start: 0.7536 (m) cc_final: 0.6855 (p) REVERT: D 525 TRP cc_start: 0.8228 (t60) cc_final: 0.7831 (t60) REVERT: D 772 TYR cc_start: 0.7983 (m-80) cc_final: 0.7782 (m-80) REVERT: D 895 TRP cc_start: 0.8118 (m-90) cc_final: 0.6532 (p-90) REVERT: D 904 TYR cc_start: 0.6130 (m-10) cc_final: 0.5711 (m-80) REVERT: D 965 SER cc_start: 0.7344 (m) cc_final: 0.6688 (p) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2520 time to fit residues: 123.9432 Evaluate side-chains 229 residues out of total 2784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.586 ------------------------------------------------------------------------------- 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: 3.9990 chunk 280 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.120143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105335 restraints weight = 76741.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105174 restraints weight = 75871.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105859 restraints weight = 63154.961| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22868 Z= 0.163 Angle : 0.522 6.929 31404 Z= 0.272 Chirality : 0.039 0.165 3868 Planarity : 0.004 0.065 3944 Dihedral : 4.203 20.499 3416 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 1.56 (0.16), residues: 2952 helix: 1.83 (0.11), residues: 2264 sheet: -2.09 (0.38), residues: 160 loop : -1.38 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 993 HIS 0.007 0.001 HIS C 844 PHE 0.029 0.001 PHE A 838 TYR 0.044 0.001 TYR B 772 ARG 0.004 0.000 ARG D 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3748.22 seconds wall clock time: 68 minutes 14.95 seconds (4094.95 seconds total)