Starting phenix.real_space_refine on Thu Sep 18 18:01:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lvt_23542/09_2025/7lvt_23542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lvt_23542/09_2025/7lvt_23542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lvt_23542/09_2025/7lvt_23542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lvt_23542/09_2025/7lvt_23542.map" model { file = "/net/cci-nas-00/data/ceres_data/7lvt_23542/09_2025/7lvt_23542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lvt_23542/09_2025/7lvt_23542.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.063 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 68 5.16 5 C 11816 2.51 5 N 3448 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18944 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 690} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Chain: "B" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 691} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Chain: "C" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 689} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Chain: "D" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 691} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Time building chain proxies: 4.81, per 1000 atoms: 0.25 Number of scatterers: 18944 At special positions: 0 Unit cell: (124.944, 162.208, 187.416, 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 68 16.00 O 3612 8.00 N 3448 7.00 C 11816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.4 microseconds 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5416 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 37 sheets defined 50.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.946A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.544A pdb=" N LEU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Proline residue: A 192 - end of helix Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.319A pdb=" N GLU A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 355 through 365 removed outlier: 4.145A pdb=" N ASN A 361 " --> pdb=" O PRO A 357 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 removed outlier: 3.638A pdb=" N ASN A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 removed outlier: 3.649A pdb=" N LEU A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.625A pdb=" N VAL A 579 " --> pdb=" O CYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 661 removed outlier: 3.995A pdb=" N VAL A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'A' and resid 738 through 746 Processing helix chain 'A' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS A 776 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 3.858A pdb=" N PHE A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 removed outlier: 3.804A pdb=" N LEU A 830 " --> pdb=" O LEU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.547A pdb=" N ALA A 837 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 838 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.515A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 4.336A pdb=" N ALA B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 498 through 506 Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 559 through 581 removed outlier: 4.128A pdb=" N LEU B 567 " --> pdb=" O TRP B 563 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 574 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 579 " --> pdb=" O CYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 664 removed outlier: 3.966A pdb=" N ILE B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE B 642 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 664 " --> pdb=" O VAL B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 698 through 711 Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 719 through 730 Processing helix chain 'B' and resid 738 through 746 Processing helix chain 'B' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS B 776 " --> pdb=" O PRO B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET B 792 " --> pdb=" O GLY B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 822 through 835 removed outlier: 3.682A pdb=" N LEU B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 835 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.702A pdb=" N LEU C 55 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.752A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 178 through 191 removed outlier: 5.471A pdb=" N GLU C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.718A pdb=" N ALA C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.021A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.568A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS C 524 " --> pdb=" O TYR C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 556 removed outlier: 3.638A pdb=" N ASN C 556 " --> pdb=" O PHE C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 575 removed outlier: 3.648A pdb=" N LEU C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.590A pdb=" N VAL C 579 " --> pdb=" O CYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 661 removed outlier: 3.944A pdb=" N VAL C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 698 through 711 Processing helix chain 'C' and resid 711 through 716 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 738 through 746 Processing helix chain 'C' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS C 776 " --> pdb=" O PRO C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET C 792 " --> pdb=" O GLY C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 3.859A pdb=" N PHE C 823 " --> pdb=" O ILE C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 833 removed outlier: 3.805A pdb=" N LEU C 830 " --> pdb=" O LEU C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 838 removed outlier: 3.504A pdb=" N ALA C 837 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 838 " --> pdb=" O PHE C 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 834 through 838' Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 246 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.877A pdb=" N ALA D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.594A pdb=" N LYS D 524 " --> pdb=" O TYR D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 559 through 581 removed outlier: 4.128A pdb=" N LEU D 567 " --> pdb=" O TRP D 563 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 574 " --> pdb=" O CYS D 570 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 579 " --> pdb=" O CYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 664 removed outlier: 4.079A pdb=" N ILE D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE D 642 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 664 " --> pdb=" O VAL D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 698 through 711 Processing helix chain 'D' and resid 711 through 716 Processing helix chain 'D' and resid 719 through 730 Processing helix chain 'D' and resid 738 through 746 Processing helix chain 'D' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS D 776 " --> pdb=" O PRO D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 821 Processing helix chain 'D' and resid 822 through 835 removed outlier: 3.674A pdb=" N LEU D 830 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL D 831 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 835 " --> pdb=" O VAL D 831 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80 removed outlier: 3.562A pdb=" N ILE A 38 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N ALA A 105 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE A 107 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY A 39 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A 129 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A 384 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 150 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 201 removed outlier: 4.350A pdb=" N TYR A 225 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA4, first strand: chain 'A' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU A 433 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 435 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AA7, first strand: chain 'A' and resid 533 through 535 removed outlier: 3.928A pdb=" N MET A 533 " --> pdb=" O TYR A 763 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 682 removed outlier: 6.572A pdb=" N GLU A 680 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 735 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 682 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU A 737 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 539 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.036A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLN B 81 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 131 removed outlier: 8.056A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASN B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.277A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.277A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB5, first strand: chain 'B' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU B 433 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS B 481 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 435 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'B' and resid 526 through 528 Processing sheet with id=AB8, first strand: chain 'B' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET B 533 " --> pdb=" O TYR B 763 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.572A pdb=" N GLU B 680 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 735 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY B 682 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU B 737 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 539 " --> pdb=" O ILE B 754 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 76 through 83 removed outlier: 6.235A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN C 81 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 201 through 203 removed outlier: 7.821A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 256 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 279 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 389 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 404 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AC5, first strand: chain 'C' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU C 433 " --> pdb=" O ASP C 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL C 435 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'C' and resid 526 through 528 Processing sheet with id=AC8, first strand: chain 'C' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET C 533 " --> pdb=" O TYR C 763 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.573A pdb=" N GLU C 680 " --> pdb=" O ALA C 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 735 " --> pdb=" O GLU C 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY C 682 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU C 737 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 539 " --> pdb=" O ILE C 754 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 75 through 83 Processing sheet with id=AD2, first strand: chain 'D' and resid 129 through 131 removed outlier: 7.992A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASN D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.436A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AD5, first strand: chain 'D' and resid 388 through 395 removed outlier: 3.690A pdb=" N GLY D 403 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS D 395 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 404 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU D 433 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL D 435 " --> pdb=" O LYS D 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 528 Processing sheet with id=AD9, first strand: chain 'D' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET D 533 " --> pdb=" O TYR D 763 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.574A pdb=" N GLU D 680 " --> pdb=" O ALA D 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 735 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY D 682 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU D 737 " --> pdb=" O GLY D 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 539 " --> pdb=" O ILE D 754 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3343 1.31 - 1.44: 4746 1.44 - 1.56: 10956 1.56 - 1.68: 39 1.68 - 1.81: 120 Bond restraints: 19204 Sorted by residual: bond pdb=" C TRP C 296 " pdb=" O TRP C 296 " ideal model delta sigma weight residual 1.237 1.318 -0.081 1.17e-02 7.31e+03 4.84e+01 bond pdb=" C PRO B 304 " pdb=" O PRO B 304 " ideal model delta sigma weight residual 1.240 1.187 0.053 1.12e-02 7.97e+03 2.26e+01 bond pdb=" N ARG C 300 " pdb=" CA ARG C 300 " ideal model delta sigma weight residual 1.457 1.514 -0.056 1.29e-02 6.01e+03 1.91e+01 bond pdb=" C GLU D 267 " pdb=" O GLU D 267 " ideal model delta sigma weight residual 1.237 1.288 -0.052 1.19e-02 7.06e+03 1.89e+01 bond pdb=" C LEU B 301 " pdb=" O LEU B 301 " ideal model delta sigma weight residual 1.233 1.287 -0.054 1.46e-02 4.69e+03 1.37e+01 ... (remaining 19199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 23327 2.10 - 4.19: 2465 4.19 - 6.29: 364 6.29 - 8.39: 63 8.39 - 10.48: 17 Bond angle restraints: 26236 Sorted by residual: angle pdb=" N PRO B 304 " pdb=" CA PRO B 304 " pdb=" C PRO B 304 " ideal model delta sigma weight residual 110.70 100.22 10.48 1.22e+00 6.72e-01 7.38e+01 angle pdb=" N SER D 738 " pdb=" CA SER D 738 " pdb=" C SER D 738 " ideal model delta sigma weight residual 111.75 121.99 -10.24 1.28e+00 6.10e-01 6.40e+01 angle pdb=" N SER C 738 " pdb=" CA SER C 738 " pdb=" C SER C 738 " ideal model delta sigma weight residual 111.75 121.98 -10.23 1.28e+00 6.10e-01 6.39e+01 angle pdb=" N SER B 738 " pdb=" CA SER B 738 " pdb=" C SER B 738 " ideal model delta sigma weight residual 111.75 121.98 -10.23 1.28e+00 6.10e-01 6.38e+01 angle pdb=" N SER A 738 " pdb=" CA SER A 738 " pdb=" C SER A 738 " ideal model delta sigma weight residual 111.75 121.93 -10.18 1.28e+00 6.10e-01 6.32e+01 ... (remaining 26231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 10453 16.98 - 33.95: 783 33.95 - 50.93: 155 50.93 - 67.91: 23 67.91 - 84.88: 6 Dihedral angle restraints: 11420 sinusoidal: 3088 harmonic: 8332 Sorted by residual: dihedral pdb=" CA GLU C 48 " pdb=" C GLU C 48 " pdb=" N PRO C 49 " pdb=" CA PRO C 49 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" C GLU D 48 " pdb=" N GLU D 48 " pdb=" CA GLU D 48 " pdb=" CB GLU D 48 " ideal model delta harmonic sigma weight residual -122.60 -136.79 14.19 0 2.50e+00 1.60e-01 3.22e+01 dihedral pdb=" CA ILE D 638 " pdb=" C ILE D 638 " pdb=" N TRP D 639 " pdb=" CA TRP D 639 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 11417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2363 0.092 - 0.185: 590 0.185 - 0.277: 174 0.277 - 0.369: 34 0.369 - 0.461: 3 Chirality restraints: 3164 Sorted by residual: chirality pdb=" CA PHE C 583 " pdb=" N PHE C 583 " pdb=" C PHE C 583 " pdb=" CB PHE C 583 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CA GLU D 48 " pdb=" N GLU D 48 " pdb=" C GLU D 48 " pdb=" CB GLU D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 3161 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 178 " 0.027 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C ASP A 178 " -0.098 2.00e-02 2.50e+03 pdb=" O ASP A 178 " 0.037 2.00e-02 2.50e+03 pdb=" N SER A 179 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 297 " -0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C SER B 297 " 0.088 2.00e-02 2.50e+03 pdb=" O SER B 297 " -0.033 2.00e-02 2.50e+03 pdb=" N MET B 298 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 298 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C MET B 298 " -0.067 2.00e-02 2.50e+03 pdb=" O MET B 298 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 299 " 0.023 2.00e-02 2.50e+03 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 236 2.63 - 3.19: 16783 3.19 - 3.76: 29198 3.76 - 4.33: 36625 4.33 - 4.90: 60629 Nonbonded interactions: 143471 Sorted by model distance: nonbonded pdb=" CB ALA B 706 " pdb=" O LYS C 697 " model vdw 2.057 3.460 nonbonded pdb=" O MET A 247 " pdb=" OH TYR A 254 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP B 260 " pdb=" OG1 THR B 318 " model vdw 2.306 3.040 nonbonded pdb=" O LYS A 385 " pdb=" OG SER A 407 " model vdw 2.309 3.040 nonbonded pdb=" O ALA D 100 " pdb=" OG SER D 344 " model vdw 2.319 3.040 ... (remaining 143466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.100 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 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 : 0.008 0.081 19208 Z= 0.520 Angle : 1.359 10.481 26244 Z= 0.950 Chirality : 0.092 0.461 3164 Planarity : 0.007 0.074 3496 Dihedral : 13.036 84.885 5992 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.40 % Favored : 93.32 % Rotamer: Outliers : 0.96 % Allowed : 9.25 % Favored : 89.79 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.14), residues: 2828 helix: -1.41 (0.12), residues: 1321 sheet: -2.48 (0.21), residues: 468 loop : -2.19 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 306 TYR 0.037 0.002 TYR A 328 PHE 0.035 0.002 PHE B 59 TRP 0.014 0.002 TRP D 368 HIS 0.016 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00777 (19204) covalent geometry : angle 1.35906 (26236) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.83552 ( 8) hydrogen bonds : bond 0.15644 ( 1081) hydrogen bonds : angle 7.11802 ( 3141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9472 (mt) cc_final: 0.9170 (mp) REVERT: A 132 THR cc_start: 0.8792 (p) cc_final: 0.8323 (t) REVERT: A 166 TYR cc_start: 0.9110 (t80) cc_final: 0.8627 (t80) REVERT: A 196 ASN cc_start: 0.8372 (p0) cc_final: 0.8003 (p0) REVERT: A 250 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6108 (pt0) REVERT: A 282 LEU cc_start: 0.9689 (mm) cc_final: 0.9484 (mm) outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.0702 time to fit residues: 8.4610 Evaluate side-chains 59 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054234 restraints weight = 22770.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.055954 restraints weight = 12470.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057149 restraints weight = 8054.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057887 restraints weight = 5816.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058478 restraints weight = 4644.081| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4431 moved from start: 7.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 19208 Z= 0.397 Angle : 1.094 16.213 26244 Z= 0.705 Chirality : 0.058 0.586 3164 Planarity : 0.007 0.087 3496 Dihedral : 8.419 154.667 3008 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 2.12 % Allowed : 5.66 % Favored : 92.22 % Rotamer: Outliers : 0.89 % Allowed : 7.10 % Favored : 92.01 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.15), residues: 2828 helix: 0.01 (0.14), residues: 1288 sheet: -2.38 (0.20), residues: 492 loop : -2.27 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 133 TYR 0.015 0.002 TYR B 166 PHE 0.013 0.001 PHE B 262 TRP 0.015 0.002 TRP D 405 HIS 0.011 0.002 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00593 (19204) covalent geometry : angle 1.09207 (26236) SS BOND : bond 0.02882 ( 4) SS BOND : angle 4.26033 ( 8) hydrogen bonds : bond 0.21794 ( 1081) hydrogen bonds : angle 7.22820 ( 3141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8944 (p) cc_final: 0.8249 (p) REVERT: A 143 ASP cc_start: 0.7987 (m-30) cc_final: 0.7179 (m-30) REVERT: A 166 TYR cc_start: 0.9038 (t80) cc_final: 0.8807 (t80) REVERT: A 196 ASN cc_start: 0.8496 (p0) cc_final: 0.8233 (p0) REVERT: A 221 SER cc_start: 0.8901 (t) cc_final: 0.8641 (p) REVERT: A 250 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6840 (pt0) REVERT: A 323 MET cc_start: 0.9619 (tpp) cc_final: 0.9263 (mmm) REVERT: A 325 ASP cc_start: 0.9182 (m-30) cc_final: 0.8920 (m-30) REVERT: A 385 LYS cc_start: 0.8445 (mmtm) cc_final: 0.7780 (tttt) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.0469 time to fit residues: 4.5209 Evaluate side-chains 47 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 280 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 233 optimal weight: 0.2980 chunk 271 optimal weight: 30.0000 chunk 270 optimal weight: 30.0000 chunk 279 optimal weight: 0.0970 chunk 192 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN C 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.074918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057142 restraints weight = 22590.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.058873 restraints weight = 12835.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060105 restraints weight = 8509.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060949 restraints weight = 6226.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061458 restraints weight = 4958.584| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4410 moved from start: 7.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19208 Z= 0.253 Angle : 0.810 12.201 26244 Z= 0.497 Chirality : 0.044 0.248 3164 Planarity : 0.006 0.056 3496 Dihedral : 7.209 136.487 3008 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.53 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.16), residues: 2828 helix: 0.61 (0.14), residues: 1340 sheet: -1.86 (0.24), residues: 396 loop : -1.71 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 374 TYR 0.028 0.002 TYR D 324 PHE 0.013 0.001 PHE D 262 TRP 0.009 0.001 TRP D 368 HIS 0.008 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00387 (19204) covalent geometry : angle 0.80924 (26236) SS BOND : bond 0.00725 ( 4) SS BOND : angle 1.50215 ( 8) hydrogen bonds : bond 0.11184 ( 1081) hydrogen bonds : angle 6.02557 ( 3141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: C 53 GLU cc_start: 0.8912 (pt0) cc_final: 0.8658 (mt-10) REVERT: C 143 ASP cc_start: 0.7269 (m-30) cc_final: 0.6567 (m-30) REVERT: C 182 LEU cc_start: 0.9169 (tp) cc_final: 0.8824 (tp) REVERT: C 221 SER cc_start: 0.8732 (t) cc_final: 0.8422 (p) REVERT: C 325 ASP cc_start: 0.9091 (m-30) cc_final: 0.8834 (m-30) REVERT: C 385 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7423 (tttt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0506 time to fit residues: 4.3334 Evaluate side-chains 45 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 10 optimal weight: 0.1980 chunk 138 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.0970 chunk 206 optimal weight: 30.0000 chunk 178 optimal weight: 0.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057116 restraints weight = 22598.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.058866 restraints weight = 12943.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060083 restraints weight = 8606.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060929 restraints weight = 6317.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061466 restraints weight = 5046.011| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4427 moved from start: 7.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19208 Z= 0.178 Angle : 0.674 8.646 26244 Z= 0.406 Chirality : 0.041 0.153 3164 Planarity : 0.004 0.034 3496 Dihedral : 6.780 137.365 3008 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.37 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2828 helix: 0.85 (0.14), residues: 1380 sheet: -1.54 (0.24), residues: 460 loop : -1.55 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.025 0.001 TYR D 324 PHE 0.009 0.001 PHE A 42 TRP 0.006 0.001 TRP D 405 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00300 (19204) covalent geometry : angle 0.67371 (26236) SS BOND : bond 0.00501 ( 4) SS BOND : angle 1.09563 ( 8) hydrogen bonds : bond 0.07949 ( 1081) hydrogen bonds : angle 5.75942 ( 3141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.174 Fit side-chains REVERT: C 53 GLU cc_start: 0.8873 (pt0) cc_final: 0.8578 (mt-10) REVERT: C 176 TYR cc_start: 0.8088 (p90) cc_final: 0.7770 (p90) REVERT: C 182 LEU cc_start: 0.9177 (tp) cc_final: 0.8930 (tp) REVERT: C 200 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7452 (tptt) REVERT: C 221 SER cc_start: 0.8689 (t) cc_final: 0.8394 (p) REVERT: C 325 ASP cc_start: 0.9132 (m-30) cc_final: 0.8830 (m-30) REVERT: C 385 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7306 (tttt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0527 time to fit residues: 4.0769 Evaluate side-chains 41 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 281 optimal weight: 20.0000 chunk 118 optimal weight: 40.0000 chunk 90 optimal weight: 0.0040 chunk 38 optimal weight: 20.0000 chunk 195 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 104 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 199 optimal weight: 40.0000 overall best weight: 1.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.056862 restraints weight = 23134.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058669 restraints weight = 13112.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059905 restraints weight = 8588.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.060772 restraints weight = 6294.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061384 restraints weight = 5002.320| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4464 moved from start: 7.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19208 Z= 0.166 Angle : 0.665 7.939 26244 Z= 0.397 Chirality : 0.041 0.148 3164 Planarity : 0.004 0.028 3496 Dihedral : 6.809 135.903 3008 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.09 % Favored : 94.63 % Rotamer: Outliers : 0.30 % Allowed : 2.66 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2828 helix: 1.09 (0.14), residues: 1376 sheet: -1.45 (0.25), residues: 440 loop : -1.33 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.019 0.001 TYR B 324 PHE 0.011 0.001 PHE B 42 TRP 0.007 0.001 TRP D 405 HIS 0.003 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00289 (19204) covalent geometry : angle 0.66454 (26236) SS BOND : bond 0.00350 ( 4) SS BOND : angle 1.03102 ( 8) hydrogen bonds : bond 0.07430 ( 1081) hydrogen bonds : angle 5.54161 ( 3141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.198 Fit side-chains REVERT: C 132 THR cc_start: 0.8804 (p) cc_final: 0.8311 (p) REVERT: C 176 TYR cc_start: 0.8350 (p90) cc_final: 0.8104 (p90) REVERT: C 182 LEU cc_start: 0.9137 (tp) cc_final: 0.8897 (tp) REVERT: C 200 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7433 (tptt) REVERT: C 221 SER cc_start: 0.8753 (t) cc_final: 0.8437 (p) REVERT: C 237 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8453 (tm-30) REVERT: C 325 ASP cc_start: 0.9070 (m-30) cc_final: 0.8842 (m-30) REVERT: C 385 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7290 (tttt) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0487 time to fit residues: 4.2572 Evaluate side-chains 45 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 127 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 chunk 118 optimal weight: 40.0000 chunk 49 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 62 optimal weight: 0.0370 overall best weight: 2.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.056607 restraints weight = 23145.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.058349 restraints weight = 13189.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.059627 restraints weight = 8804.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060398 restraints weight = 6433.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061112 restraints weight = 5168.226| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4498 moved from start: 7.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19208 Z= 0.177 Angle : 0.665 8.220 26244 Z= 0.396 Chirality : 0.041 0.152 3164 Planarity : 0.004 0.033 3496 Dihedral : 6.751 137.242 3008 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.37 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.16), residues: 2828 helix: 1.17 (0.14), residues: 1376 sheet: -1.51 (0.26), residues: 376 loop : -1.31 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 142 TYR 0.032 0.002 TYR D 324 PHE 0.012 0.001 PHE C 57 TRP 0.007 0.001 TRP D 405 HIS 0.003 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00329 (19204) covalent geometry : angle 0.66447 (26236) SS BOND : bond 0.00173 ( 4) SS BOND : angle 1.25588 ( 8) hydrogen bonds : bond 0.07329 ( 1081) hydrogen bonds : angle 5.48997 ( 3141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.185 Fit side-chains REVERT: C 182 LEU cc_start: 0.9070 (tp) cc_final: 0.8863 (tp) REVERT: C 200 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7360 (tptt) REVERT: C 221 SER cc_start: 0.8709 (t) cc_final: 0.8443 (p) REVERT: C 237 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8390 (tm-30) REVERT: C 324 TYR cc_start: 0.8916 (t80) cc_final: 0.8192 (t80) REVERT: C 385 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7125 (mtmt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0537 time to fit residues: 4.1855 Evaluate side-chains 42 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 87 optimal weight: 0.0000 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 119 optimal weight: 0.5980 chunk 49 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 187 optimal weight: 0.0770 chunk 241 optimal weight: 0.6980 chunk 266 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 overall best weight: 0.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.058564 restraints weight = 22860.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060413 restraints weight = 13083.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061516 restraints weight = 8668.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062510 restraints weight = 6461.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063038 restraints weight = 5101.816| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4433 moved from start: 7.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19208 Z= 0.155 Angle : 0.652 8.311 26244 Z= 0.384 Chirality : 0.040 0.157 3164 Planarity : 0.004 0.030 3496 Dihedral : 6.660 137.974 3008 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2828 helix: 1.26 (0.14), residues: 1384 sheet: -1.52 (0.25), residues: 436 loop : -1.16 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 300 TYR 0.026 0.001 TYR D 324 PHE 0.007 0.001 PHE B 244 TRP 0.010 0.001 TRP D 368 HIS 0.002 0.000 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00261 (19204) covalent geometry : angle 0.65191 (26236) SS BOND : bond 0.00250 ( 4) SS BOND : angle 1.17233 ( 8) hydrogen bonds : bond 0.07083 ( 1081) hydrogen bonds : angle 5.41131 ( 3141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.184 Fit side-chains REVERT: C 53 GLU cc_start: 0.8846 (pt0) cc_final: 0.8644 (pm20) REVERT: C 110 SER cc_start: 0.9031 (t) cc_final: 0.8665 (p) REVERT: C 176 TYR cc_start: 0.8643 (p90) cc_final: 0.8191 (p90) REVERT: C 182 LEU cc_start: 0.9146 (tp) cc_final: 0.8891 (tp) REVERT: C 200 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7454 (tptt) REVERT: C 221 SER cc_start: 0.8738 (t) cc_final: 0.8452 (p) REVERT: C 237 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 245 MET cc_start: 0.8725 (tmm) cc_final: 0.8476 (tmm) REVERT: C 324 TYR cc_start: 0.8844 (t80) cc_final: 0.8106 (t80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0469 time to fit residues: 4.2488 Evaluate side-chains 46 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 0.0030 chunk 217 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 265 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 37 optimal weight: 0.0000 chunk 229 optimal weight: 0.0470 overall best weight: 0.6094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.076561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.058165 restraints weight = 23042.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059955 restraints weight = 13356.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061207 restraints weight = 8919.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.062011 restraints weight = 6565.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062714 restraints weight = 5269.347| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4456 moved from start: 7.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19208 Z= 0.151 Angle : 0.633 8.219 26244 Z= 0.376 Chirality : 0.040 0.153 3164 Planarity : 0.004 0.029 3496 Dihedral : 6.562 137.715 3008 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.95 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.17), residues: 2828 helix: 1.44 (0.15), residues: 1380 sheet: -1.36 (0.25), residues: 432 loop : -1.14 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 142 TYR 0.021 0.001 TYR D 324 PHE 0.014 0.001 PHE A 255 TRP 0.024 0.001 TRP D 296 HIS 0.002 0.000 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00255 (19204) covalent geometry : angle 0.63279 (26236) SS BOND : bond 0.00965 ( 4) SS BOND : angle 1.42297 ( 8) hydrogen bonds : bond 0.06929 ( 1081) hydrogen bonds : angle 5.33495 ( 3141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.196 Fit side-chains REVERT: C 132 THR cc_start: 0.8575 (p) cc_final: 0.8270 (p) REVERT: C 176 TYR cc_start: 0.8751 (p90) cc_final: 0.8193 (p90) REVERT: C 182 LEU cc_start: 0.9146 (tp) cc_final: 0.8903 (tp) REVERT: C 200 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7431 (tptt) REVERT: C 221 SER cc_start: 0.8735 (t) cc_final: 0.8503 (p) REVERT: C 237 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8534 (tm-30) REVERT: C 247 MET cc_start: 0.8999 (tpp) cc_final: 0.8727 (tpp) REVERT: C 323 MET cc_start: 0.9594 (mmm) cc_final: 0.9305 (mmm) REVERT: C 324 TYR cc_start: 0.8814 (t80) cc_final: 0.8240 (t80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0494 time to fit residues: 4.2946 Evaluate side-chains 43 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 164 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 186 optimal weight: 40.0000 chunk 234 optimal weight: 0.0270 chunk 106 optimal weight: 0.4980 chunk 227 optimal weight: 0.0770 chunk 92 optimal weight: 0.0000 chunk 15 optimal weight: 1.9990 chunk 247 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 188 optimal weight: 0.0060 overall best weight: 0.1216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.077641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.059547 restraints weight = 22685.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061256 restraints weight = 13476.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062519 restraints weight = 9164.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063141 restraints weight = 6801.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063961 restraints weight = 5600.178| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4421 moved from start: 7.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19208 Z= 0.156 Angle : 0.660 7.746 26244 Z= 0.385 Chirality : 0.040 0.151 3164 Planarity : 0.004 0.030 3496 Dihedral : 6.592 137.499 3008 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.09 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2828 helix: 1.38 (0.15), residues: 1388 sheet: -1.25 (0.26), residues: 432 loop : -1.20 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 300 TYR 0.018 0.001 TYR A 328 PHE 0.011 0.001 PHE C 255 TRP 0.018 0.001 TRP D 296 HIS 0.001 0.000 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00264 (19204) covalent geometry : angle 0.66007 (26236) SS BOND : bond 0.00316 ( 4) SS BOND : angle 1.49529 ( 8) hydrogen bonds : bond 0.06885 ( 1081) hydrogen bonds : angle 5.32942 ( 3141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.156 Fit side-chains REVERT: C 132 THR cc_start: 0.8574 (p) cc_final: 0.8231 (p) REVERT: C 200 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7476 (tptt) REVERT: C 221 SER cc_start: 0.8784 (t) cc_final: 0.8528 (p) REVERT: C 237 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8581 (tm-30) REVERT: C 323 MET cc_start: 0.9586 (mmm) cc_final: 0.9291 (mmm) REVERT: C 324 TYR cc_start: 0.8835 (t80) cc_final: 0.8255 (t80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0482 time to fit residues: 4.1984 Evaluate side-chains 45 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 61 optimal weight: 30.0000 chunk 226 optimal weight: 0.0570 chunk 245 optimal weight: 0.0370 chunk 111 optimal weight: 0.0010 chunk 234 optimal weight: 0.2980 chunk 228 optimal weight: 0.0050 chunk 77 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.078345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061239 restraints weight = 22852.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.062760 restraints weight = 14408.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.063827 restraints weight = 10148.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.064582 restraints weight = 7769.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.065181 restraints weight = 6357.474| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4402 moved from start: 7.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19208 Z= 0.154 Angle : 0.666 7.239 26244 Z= 0.385 Chirality : 0.040 0.143 3164 Planarity : 0.004 0.030 3496 Dihedral : 6.606 137.306 3008 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.17), residues: 2828 helix: 1.40 (0.15), residues: 1388 sheet: -1.15 (0.25), residues: 440 loop : -1.14 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.018 0.001 TYR D 324 PHE 0.010 0.001 PHE C 255 TRP 0.007 0.001 TRP C 134 HIS 0.001 0.000 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00265 (19204) covalent geometry : angle 0.66574 (26236) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.42000 ( 8) hydrogen bonds : bond 0.06765 ( 1081) hydrogen bonds : angle 5.31622 ( 3141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.235 Fit side-chains REVERT: C 176 TYR cc_start: 0.8051 (p90) cc_final: 0.7807 (p90) REVERT: C 186 GLN cc_start: 0.8468 (tt0) cc_final: 0.8251 (tp-100) REVERT: C 217 GLU cc_start: 0.9263 (tp30) cc_final: 0.8843 (tp30) REVERT: C 221 SER cc_start: 0.8768 (t) cc_final: 0.8453 (p) REVERT: C 324 TYR cc_start: 0.8731 (t80) cc_final: 0.8140 (t80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0461 time to fit residues: 4.4230 Evaluate side-chains 47 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 224 optimal weight: 0.6980 chunk 207 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 204 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.0030 chunk 247 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 193 optimal weight: 20.0000 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060115 restraints weight = 23090.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061940 restraints weight = 13801.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063227 restraints weight = 9385.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064137 restraints weight = 6999.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064772 restraints weight = 5593.468| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4415 moved from start: 7.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19208 Z= 0.154 Angle : 0.663 9.251 26244 Z= 0.382 Chirality : 0.040 0.146 3164 Planarity : 0.004 0.029 3496 Dihedral : 6.667 136.756 3008 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.16), residues: 2828 helix: 1.43 (0.15), residues: 1376 sheet: -0.89 (0.26), residues: 440 loop : -1.10 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 133 TYR 0.013 0.001 TYR B 328 PHE 0.009 0.001 PHE D 377 TRP 0.004 0.001 TRP A 296 HIS 0.002 0.000 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00266 (19204) covalent geometry : angle 0.66297 (26236) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.39110 ( 8) hydrogen bonds : bond 0.06706 ( 1081) hydrogen bonds : angle 5.32091 ( 3141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.80 seconds wall clock time: 26 minutes 48.18 seconds (1608.18 seconds total)