Starting phenix.real_space_refine on Wed Mar 4 08:14:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjy_33237/03_2026/7xjy_33237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjy_33237/03_2026/7xjy_33237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjy_33237/03_2026/7xjy_33237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjy_33237/03_2026/7xjy_33237.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjy_33237/03_2026/7xjy_33237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjy_33237/03_2026/7xjy_33237.cif" } resolution = 3.6 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= -0.001 sd= 0.133 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 48 5.16 5 C 7713 2.51 5 N 2061 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12070 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6034 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 727} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6036 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 727} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 2.64, per 1000 atoms: 0.22 Number of scatterers: 12070 At special positions: 0 Unit cell: (150.7, 122.1, 86.9, 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 48 16.00 O 2248 8.00 N 2061 7.00 C 7713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 493.7 milliseconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 16 sheets defined 54.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.834A pdb=" N ALA A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A 47 " --> pdb=" O TRP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.545A pdb=" N SER A 91 " --> pdb=" O PRO A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.502A pdb=" N GLY A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.512A pdb=" N ASN A 205 " --> pdb=" O HIS A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 214 through 231 removed outlier: 5.540A pdb=" N GLU A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASN A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.638A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.912A pdb=" N ALA A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 311 removed outlier: 4.071A pdb=" N ARG A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 Processing helix chain 'A' and resid 466 through 480 Proline residue: A 474 - end of helix removed outlier: 3.601A pdb=" N ILE A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 541 through 549 Processing helix chain 'A' and resid 556 through 572 Processing helix chain 'A' and resid 580 through 591 removed outlier: 3.723A pdb=" N VAL A 591 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 removed outlier: 3.778A pdb=" N PHE A 605 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.685A pdb=" N LEU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 673 removed outlier: 3.591A pdb=" N VAL A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 4.003A pdb=" N PHE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 682' Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.828A pdb=" N SER A 686 " --> pdb=" O ASP A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 745 through 748 removed outlier: 3.588A pdb=" N ALA A 748 " --> pdb=" O THR A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 748' Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 762 through 772 Processing helix chain 'A' and resid 785 through 807 Processing helix chain 'A' and resid 818 through 833 removed outlier: 3.558A pdb=" N ILE A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 removed outlier: 3.503A pdb=" N GLU A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 874 Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.856A pdb=" N ALA B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 47 " --> pdb=" O TRP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.551A pdb=" N SER B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.507A pdb=" N ASN B 205 " --> pdb=" O HIS B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 214 through 231 removed outlier: 5.743A pdb=" N GLU B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.696A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.899A pdb=" N ALA B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 removed outlier: 4.093A pdb=" N ARG B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 376 Processing helix chain 'B' and resid 466 through 480 Proline residue: B 474 - end of helix removed outlier: 3.641A pdb=" N ILE B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 541 through 549 removed outlier: 3.504A pdb=" N ALA B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 572 Processing helix chain 'B' and resid 580 through 591 removed outlier: 3.747A pdb=" N VAL B 591 " --> pdb=" O VAL B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.787A pdb=" N PHE B 605 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 removed outlier: 3.697A pdb=" N LEU B 613 " --> pdb=" O PRO B 609 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 674 removed outlier: 3.595A pdb=" N VAL B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 687 removed outlier: 3.829A pdb=" N SER B 686 " --> pdb=" O ASP B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 Processing helix chain 'B' and resid 707 through 715 Processing helix chain 'B' and resid 718 through 720 No H-bonds generated for 'chain 'B' and resid 718 through 720' Processing helix chain 'B' and resid 721 through 730 Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 745 through 748 removed outlier: 3.526A pdb=" N ALA B 748 " --> pdb=" O THR B 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 748' Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 762 through 772 Processing helix chain 'B' and resid 785 through 807 Processing helix chain 'B' and resid 819 through 833 Processing helix chain 'B' and resid 838 through 850 Processing helix chain 'B' and resid 855 through 874 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.386A pdb=" N ALA A 49 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL A 82 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 165 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET A 160 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 166 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP A 152 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.386A pdb=" N ALA A 49 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL A 82 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 165 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET A 160 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 166 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP A 152 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 153 " --> pdb=" O TRP A 144 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 144 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 388 removed outlier: 4.223A pdb=" N ASN A 398 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ARG A 342 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.605A pdb=" N PHE A 514 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 577 removed outlier: 6.923A pdb=" N PHE A 624 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N CYS A 637 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL A 626 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 3.578A pdb=" N HIS A 691 " --> pdb=" O GLY A 695 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.345A pdb=" N ALA B 49 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N VAL B 82 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 165 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 160 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 166 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 152 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.345A pdb=" N ALA B 49 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N VAL B 82 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 165 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 160 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 166 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 152 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 153 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 144 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AB3, first strand: chain 'B' and resid 383 through 388 removed outlier: 4.202A pdb=" N ASN B 398 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ARG B 342 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 514 removed outlier: 3.599A pdb=" N PHE B 514 " --> pdb=" O ILE B 517 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 522 through 524 Processing sheet with id=AB6, first strand: chain 'B' and resid 575 through 577 removed outlier: 6.994A pdb=" N PHE B 624 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N CYS B 637 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B 626 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 689 through 691 removed outlier: 3.710A pdb=" N HIS B 691 " --> pdb=" O GLY B 695 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2058 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: 1.93 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2035 1.27 - 1.41: 2971 1.41 - 1.54: 7217 1.54 - 1.68: 15 1.68 - 1.81: 82 Bond restraints: 12320 Sorted by residual: bond pdb=" C TYR B 208 " pdb=" O TYR B 208 " ideal model delta sigma weight residual 1.236 1.140 0.097 1.15e-02 7.56e+03 7.05e+01 bond pdb=" C GLN A 33 " pdb=" N GLN A 34 " ideal model delta sigma weight residual 1.335 1.269 0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" C GLN A 33 " pdb=" O GLN A 33 " ideal model delta sigma weight residual 1.236 1.181 0.054 1.29e-02 6.01e+03 1.78e+01 bond pdb=" CA THR B 209 " pdb=" C THR B 209 " ideal model delta sigma weight residual 1.522 1.470 0.051 1.24e-02 6.50e+03 1.72e+01 bond pdb=" C THR B 209 " pdb=" N LYS B 210 " ideal model delta sigma weight residual 1.332 1.278 0.055 1.40e-02 5.10e+03 1.52e+01 ... (remaining 12315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 15922 1.99 - 3.99: 626 3.99 - 5.98: 130 5.98 - 7.97: 21 7.97 - 9.97: 5 Bond angle restraints: 16704 Sorted by residual: angle pdb=" N GLY A 807 " pdb=" CA GLY A 807 " pdb=" C GLY A 807 " ideal model delta sigma weight residual 111.85 120.10 -8.25 1.20e+00 6.94e-01 4.73e+01 angle pdb=" N GLY B 807 " pdb=" CA GLY B 807 " pdb=" C GLY B 807 " ideal model delta sigma weight residual 111.63 118.57 -6.94 1.15e+00 7.56e-01 3.64e+01 angle pdb=" CA GLY B 807 " pdb=" C GLY B 807 " pdb=" O GLY B 807 " ideal model delta sigma weight residual 122.16 117.36 4.80 8.20e-01 1.49e+00 3.43e+01 angle pdb=" CA GLY A 807 " pdb=" C GLY A 807 " pdb=" O GLY A 807 " ideal model delta sigma weight residual 122.13 117.20 4.93 8.90e-01 1.26e+00 3.07e+01 angle pdb=" N ASP A 673 " pdb=" CA ASP A 673 " pdb=" C ASP A 673 " ideal model delta sigma weight residual 112.93 106.76 6.17 1.12e+00 7.97e-01 3.04e+01 ... (remaining 16699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6694 17.55 - 35.10: 537 35.10 - 52.65: 139 52.65 - 70.20: 44 70.20 - 87.76: 8 Dihedral angle restraints: 7422 sinusoidal: 3004 harmonic: 4418 Sorted by residual: dihedral pdb=" CA LYS B 647 " pdb=" C LYS B 647 " pdb=" N GLU B 648 " pdb=" CA GLU B 648 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LYS A 647 " pdb=" C LYS A 647 " pdb=" N GLU A 648 " pdb=" CA GLU A 648 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" C MET A 672 " pdb=" N MET A 672 " pdb=" CA MET A 672 " pdb=" CB MET A 672 " ideal model delta harmonic sigma weight residual -122.60 -111.28 -11.32 0 2.50e+00 1.60e-01 2.05e+01 ... (remaining 7419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1510 0.062 - 0.125: 315 0.125 - 0.187: 46 0.187 - 0.250: 16 0.250 - 0.312: 7 Chirality restraints: 1894 Sorted by residual: chirality pdb=" CB THR B 209 " pdb=" CA THR B 209 " pdb=" OG1 THR B 209 " pdb=" CG2 THR B 209 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB THR A 209 " pdb=" CA THR A 209 " pdb=" OG1 THR A 209 " pdb=" CG2 THR A 209 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA THR B 209 " pdb=" N THR B 209 " pdb=" C THR B 209 " pdb=" CB THR B 209 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1891 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 208 " -0.058 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR A 208 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 208 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 208 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 208 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 208 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 208 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 208 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 208 " 0.054 2.00e-02 2.50e+03 2.88e-02 1.66e+01 pdb=" CG TYR B 208 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 208 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 208 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 208 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 208 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 208 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 208 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 33 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLN A 33 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A 33 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN A 34 " 0.025 2.00e-02 2.50e+03 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1232 2.74 - 3.28: 11948 3.28 - 3.82: 19021 3.82 - 4.36: 22739 4.36 - 4.90: 39436 Nonbonded interactions: 94376 Sorted by model distance: nonbonded pdb=" OE1 GLU A 347 " pdb=" OH TYR A 542 " model vdw 2.197 3.040 nonbonded pdb=" O LEU A 30 " pdb=" NE2 GLN A 198 " model vdw 2.198 3.120 nonbonded pdb=" O ASN B 833 " pdb=" NZ LYS B 835 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR A 350 " pdb=" O GLU A 351 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLU B 347 " pdb=" OH TYR B 542 " model vdw 2.217 3.040 ... (remaining 94371 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 679 or (resid 680 and (name N or name CA or nam \ e C or name O or name CB )) or resid 681 through 874)) selection = (chain 'B' and (resid 28 through 820 or (resid 821 and (name N or name CA or nam \ e C or name O or name CB )) or resid 822 through 874)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.970 Find NCS groups from input model: 0.260 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 12320 Z= 0.412 Angle : 0.936 9.965 16704 Z= 0.617 Chirality : 0.057 0.312 1894 Planarity : 0.006 0.053 2158 Dihedral : 14.445 87.755 4566 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.16 % Favored : 95.51 % Rotamer: Outliers : 7.59 % Allowed : 10.93 % Favored : 81.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1514 helix: 0.99 (0.19), residues: 750 sheet: -0.53 (0.37), residues: 184 loop : -1.12 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 561 TYR 0.058 0.004 TYR A 208 PHE 0.017 0.002 PHE A 668 TRP 0.028 0.002 TRP A 43 HIS 0.007 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00724 (12320) covalent geometry : angle 0.93556 (16704) hydrogen bonds : bond 0.15532 ( 669) hydrogen bonds : angle 6.37844 ( 2058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 232 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 125 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 253 LEU cc_start: 0.6498 (mt) cc_final: 0.6296 (mt) REVERT: A 263 ASP cc_start: 0.8084 (t70) cc_final: 0.7756 (t0) REVERT: B 30 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7449 (mp) REVERT: B 118 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: B 183 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8982 (p) REVERT: B 253 LEU cc_start: 0.6500 (mt) cc_final: 0.6260 (mt) REVERT: B 263 ASP cc_start: 0.7974 (t70) cc_final: 0.7655 (t0) REVERT: B 366 GLU cc_start: 0.7707 (tt0) cc_final: 0.7450 (tt0) REVERT: B 500 TRP cc_start: 0.6813 (OUTLIER) cc_final: 0.5403 (p-90) outliers start: 100 outliers final: 48 residues processed: 324 average time/residue: 0.1188 time to fit residues: 53.7691 Evaluate side-chains 188 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 500 TRP Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 813 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 809 GLN B 33 GLN B 98 ASN B 172 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.143318 restraints weight = 19621.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142208 restraints weight = 14464.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142977 restraints weight = 14782.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143879 restraints weight = 9051.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144338 restraints weight = 7859.586| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12320 Z= 0.134 Angle : 0.581 7.145 16704 Z= 0.309 Chirality : 0.044 0.151 1894 Planarity : 0.005 0.046 2158 Dihedral : 8.110 66.596 1727 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 3.34 % Allowed : 16.24 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1514 helix: 1.62 (0.19), residues: 750 sheet: -0.21 (0.39), residues: 186 loop : -0.67 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 796 TYR 0.016 0.002 TYR A 188 PHE 0.012 0.001 PHE B 534 TRP 0.015 0.001 TRP A 43 HIS 0.004 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00277 (12320) covalent geometry : angle 0.58079 (16704) hydrogen bonds : bond 0.04940 ( 669) hydrogen bonds : angle 4.59566 ( 2058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 252 LEU cc_start: 0.8297 (mt) cc_final: 0.8080 (mt) REVERT: A 253 LEU cc_start: 0.6401 (mt) cc_final: 0.6201 (mt) REVERT: A 744 PHE cc_start: 0.7644 (m-80) cc_final: 0.7120 (m-80) REVERT: B 30 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7061 (mp) REVERT: B 253 LEU cc_start: 0.6564 (mt) cc_final: 0.6314 (mt) REVERT: B 672 MET cc_start: 0.7448 (tmm) cc_final: 0.6878 (tmm) REVERT: B 682 ARG cc_start: 0.6478 (mtp180) cc_final: 0.6064 (mtp180) REVERT: B 684 GLN cc_start: 0.6945 (mp10) cc_final: 0.6639 (mp10) REVERT: B 697 MET cc_start: 0.6742 (mtp) cc_final: 0.6477 (mtp) REVERT: B 714 LEU cc_start: 0.6786 (mm) cc_final: 0.6586 (mt) outliers start: 44 outliers final: 22 residues processed: 203 average time/residue: 0.1148 time to fit residues: 33.5200 Evaluate side-chains 159 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.171436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142130 restraints weight = 20060.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141506 restraints weight = 15193.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142083 restraints weight = 14779.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142979 restraints weight = 9024.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143528 restraints weight = 7725.204| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12320 Z= 0.150 Angle : 0.562 7.088 16704 Z= 0.300 Chirality : 0.044 0.152 1894 Planarity : 0.005 0.050 2158 Dihedral : 6.295 59.674 1673 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 3.11 % Allowed : 17.83 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1514 helix: 1.67 (0.19), residues: 758 sheet: 0.09 (0.40), residues: 174 loop : -0.90 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 391 TYR 0.018 0.002 TYR B 188 PHE 0.013 0.001 PHE B 534 TRP 0.013 0.001 TRP A 43 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00344 (12320) covalent geometry : angle 0.56206 (16704) hydrogen bonds : bond 0.05003 ( 669) hydrogen bonds : angle 4.40556 ( 2058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 253 LEU cc_start: 0.6502 (mt) cc_final: 0.6253 (mt) REVERT: A 473 LEU cc_start: 0.7552 (mt) cc_final: 0.7347 (mt) REVERT: A 668 PHE cc_start: 0.7376 (t80) cc_final: 0.6990 (t80) REVERT: A 697 MET cc_start: 0.5659 (mtp) cc_final: 0.5324 (mtt) REVERT: A 744 PHE cc_start: 0.7733 (m-80) cc_final: 0.7242 (m-80) REVERT: B 253 LEU cc_start: 0.6596 (mt) cc_final: 0.6306 (mt) REVERT: B 552 LEU cc_start: 0.8010 (mp) cc_final: 0.7185 (tt) REVERT: B 639 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7575 (mp) REVERT: B 672 MET cc_start: 0.7431 (tmm) cc_final: 0.6838 (tmm) REVERT: B 701 MET cc_start: 0.7891 (mmm) cc_final: 0.7577 (mmm) outliers start: 41 outliers final: 26 residues processed: 190 average time/residue: 0.1053 time to fit residues: 29.6159 Evaluate side-chains 161 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.170124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140789 restraints weight = 20034.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140720 restraints weight = 14455.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141656 restraints weight = 13221.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142218 restraints weight = 9079.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142736 restraints weight = 7972.834| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12320 Z= 0.163 Angle : 0.564 7.820 16704 Z= 0.300 Chirality : 0.044 0.153 1894 Planarity : 0.005 0.048 2158 Dihedral : 5.889 58.719 1669 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 3.95 % Allowed : 17.98 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1514 helix: 1.64 (0.19), residues: 758 sheet: 0.09 (0.40), residues: 174 loop : -1.00 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 391 TYR 0.020 0.002 TYR B 188 PHE 0.015 0.001 PHE B 534 TRP 0.013 0.001 TRP A 43 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00374 (12320) covalent geometry : angle 0.56393 (16704) hydrogen bonds : bond 0.05041 ( 669) hydrogen bonds : angle 4.35670 ( 2058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7762 (mp) REVERT: A 253 LEU cc_start: 0.6524 (mt) cc_final: 0.6268 (mt) REVERT: A 634 LEU cc_start: 0.8736 (mm) cc_final: 0.8391 (mt) REVERT: A 639 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (mp) REVERT: A 668 PHE cc_start: 0.7435 (t80) cc_final: 0.7039 (t80) REVERT: A 672 MET cc_start: 0.7190 (ttm) cc_final: 0.6754 (tmm) REVERT: A 701 MET cc_start: 0.6468 (mmm) cc_final: 0.6250 (mmm) REVERT: A 743 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: A 744 PHE cc_start: 0.7756 (m-80) cc_final: 0.6897 (m-80) REVERT: B 183 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 253 LEU cc_start: 0.6690 (mt) cc_final: 0.6404 (mt) REVERT: B 672 MET cc_start: 0.7445 (tmm) cc_final: 0.6849 (tmm) REVERT: B 685 LEU cc_start: 0.7940 (tp) cc_final: 0.7657 (tp) outliers start: 52 outliers final: 35 residues processed: 180 average time/residue: 0.0995 time to fit residues: 26.7281 Evaluate side-chains 160 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 GLN A 809 GLN A 833 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139064 restraints weight = 20112.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138813 restraints weight = 14804.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139640 restraints weight = 13941.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140279 restraints weight = 9572.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142078 restraints weight = 8350.237| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12320 Z= 0.174 Angle : 0.578 7.692 16704 Z= 0.307 Chirality : 0.044 0.163 1894 Planarity : 0.005 0.066 2158 Dihedral : 5.676 59.371 1666 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 4.17 % Allowed : 18.36 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1514 helix: 1.49 (0.19), residues: 774 sheet: 0.01 (0.41), residues: 174 loop : -1.17 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 796 TYR 0.021 0.002 TYR A 188 PHE 0.015 0.001 PHE B 534 TRP 0.014 0.001 TRP B 43 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00405 (12320) covalent geometry : angle 0.57796 (16704) hydrogen bonds : bond 0.05191 ( 669) hydrogen bonds : angle 4.36422 ( 2058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7702 (mp) REVERT: A 253 LEU cc_start: 0.6547 (mt) cc_final: 0.6289 (mt) REVERT: A 634 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 639 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 668 PHE cc_start: 0.7544 (t80) cc_final: 0.7091 (t80) REVERT: A 672 MET cc_start: 0.7130 (ttm) cc_final: 0.6720 (tmm) REVERT: A 701 MET cc_start: 0.6654 (mmm) cc_final: 0.6432 (mmm) REVERT: B 183 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8707 (p) REVERT: B 253 LEU cc_start: 0.6725 (mt) cc_final: 0.6442 (mt) REVERT: B 639 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7701 (mp) REVERT: B 672 MET cc_start: 0.7448 (tmm) cc_final: 0.6845 (tmm) outliers start: 55 outliers final: 40 residues processed: 180 average time/residue: 0.0969 time to fit residues: 26.3128 Evaluate side-chains 167 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 146 optimal weight: 0.0070 chunk 126 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.172547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142991 restraints weight = 20065.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142725 restraints weight = 14533.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143082 restraints weight = 15389.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144254 restraints weight = 9329.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145693 restraints weight = 7696.596| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12320 Z= 0.106 Angle : 0.517 10.056 16704 Z= 0.269 Chirality : 0.042 0.150 1894 Planarity : 0.004 0.042 2158 Dihedral : 5.383 59.465 1664 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 2.35 % Allowed : 19.95 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1514 helix: 1.82 (0.19), residues: 760 sheet: 0.13 (0.40), residues: 182 loop : -0.76 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 796 TYR 0.012 0.001 TYR B 188 PHE 0.016 0.001 PHE A 770 TRP 0.012 0.001 TRP A 43 HIS 0.002 0.000 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00225 (12320) covalent geometry : angle 0.51710 (16704) hydrogen bonds : bond 0.03850 ( 669) hydrogen bonds : angle 4.05408 ( 2058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 253 LEU cc_start: 0.6353 (mt) cc_final: 0.6055 (mt) REVERT: A 639 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 668 PHE cc_start: 0.7479 (t80) cc_final: 0.7063 (t80) REVERT: A 672 MET cc_start: 0.6904 (ttm) cc_final: 0.6532 (tmm) REVERT: A 697 MET cc_start: 0.5874 (mtp) cc_final: 0.5661 (mtt) REVERT: B 253 LEU cc_start: 0.6510 (mt) cc_final: 0.6214 (mt) REVERT: B 618 GLN cc_start: 0.7401 (mt0) cc_final: 0.7074 (mp10) REVERT: B 639 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7574 (mp) REVERT: B 672 MET cc_start: 0.7315 (tmm) cc_final: 0.6704 (tmm) outliers start: 31 outliers final: 22 residues processed: 168 average time/residue: 0.1049 time to fit residues: 25.7575 Evaluate side-chains 156 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 0.0370 chunk 149 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.170156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140498 restraints weight = 19863.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139331 restraints weight = 14430.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140256 restraints weight = 14916.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141125 restraints weight = 9654.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.141996 restraints weight = 8443.102| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12320 Z= 0.132 Angle : 0.538 8.709 16704 Z= 0.282 Chirality : 0.043 0.166 1894 Planarity : 0.005 0.044 2158 Dihedral : 5.082 58.597 1654 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 2.66 % Allowed : 20.33 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1514 helix: 1.86 (0.19), residues: 762 sheet: 0.14 (0.40), residues: 182 loop : -0.74 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 796 TYR 0.017 0.002 TYR A 188 PHE 0.012 0.001 PHE B 534 TRP 0.012 0.001 TRP A 43 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00300 (12320) covalent geometry : angle 0.53821 (16704) hydrogen bonds : bond 0.04389 ( 669) hydrogen bonds : angle 4.08608 ( 2058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.374 Fit side-chains REVERT: A 253 LEU cc_start: 0.6460 (mt) cc_final: 0.6188 (mt) REVERT: A 639 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7681 (mp) REVERT: A 668 PHE cc_start: 0.7603 (t80) cc_final: 0.7217 (t80) REVERT: A 672 MET cc_start: 0.6998 (ttm) cc_final: 0.6600 (tmm) REVERT: A 701 MET cc_start: 0.6779 (mmm) cc_final: 0.6471 (mmm) REVERT: B 253 LEU cc_start: 0.6625 (mt) cc_final: 0.6367 (mt) REVERT: B 486 MET cc_start: 0.8006 (ptm) cc_final: 0.7690 (ptt) REVERT: B 639 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 672 MET cc_start: 0.7411 (tmm) cc_final: 0.6733 (tmm) outliers start: 35 outliers final: 31 residues processed: 162 average time/residue: 0.0977 time to fit residues: 23.5811 Evaluate side-chains 155 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139000 restraints weight = 19985.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138548 restraints weight = 14989.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139508 restraints weight = 14371.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140164 restraints weight = 9936.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142920 restraints weight = 8754.610| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12320 Z= 0.174 Angle : 0.581 8.237 16704 Z= 0.307 Chirality : 0.044 0.166 1894 Planarity : 0.005 0.059 2158 Dihedral : 5.180 59.424 1654 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 3.26 % Allowed : 20.79 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1514 helix: 1.73 (0.19), residues: 758 sheet: -0.04 (0.38), residues: 196 loop : -0.77 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 796 TYR 0.021 0.002 TYR B 188 PHE 0.025 0.002 PHE B 770 TRP 0.013 0.001 TRP B 43 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00405 (12320) covalent geometry : angle 0.58134 (16704) hydrogen bonds : bond 0.05003 ( 669) hydrogen bonds : angle 4.26250 ( 2058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.426 Fit side-chains REVERT: A 253 LEU cc_start: 0.6595 (mt) cc_final: 0.6352 (mt) REVERT: A 639 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 651 VAL cc_start: 0.7140 (OUTLIER) cc_final: 0.6888 (p) REVERT: A 668 PHE cc_start: 0.7631 (t80) cc_final: 0.7299 (t80) REVERT: A 672 MET cc_start: 0.7030 (ttm) cc_final: 0.6633 (tmm) REVERT: B 183 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8750 (p) REVERT: B 253 LEU cc_start: 0.6702 (mt) cc_final: 0.6428 (mt) REVERT: B 486 MET cc_start: 0.8115 (ptm) cc_final: 0.7866 (ptt) REVERT: B 639 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7772 (mp) REVERT: B 672 MET cc_start: 0.7440 (tmm) cc_final: 0.6769 (tmm) outliers start: 43 outliers final: 36 residues processed: 160 average time/residue: 0.0891 time to fit residues: 21.9705 Evaluate side-chains 157 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.171062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141783 restraints weight = 19962.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140970 restraints weight = 14650.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.141806 restraints weight = 14878.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142586 restraints weight = 9499.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143443 restraints weight = 8268.678| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12320 Z= 0.117 Angle : 0.534 8.122 16704 Z= 0.281 Chirality : 0.043 0.173 1894 Planarity : 0.005 0.042 2158 Dihedral : 5.013 59.812 1654 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 2.73 % Allowed : 21.40 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1514 helix: 1.79 (0.19), residues: 766 sheet: 0.22 (0.40), residues: 182 loop : -0.71 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 391 TYR 0.014 0.001 TYR B 188 PHE 0.031 0.001 PHE A 770 TRP 0.014 0.001 TRP B 43 HIS 0.002 0.000 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00257 (12320) covalent geometry : angle 0.53423 (16704) hydrogen bonds : bond 0.04022 ( 669) hydrogen bonds : angle 4.07875 ( 2058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.426 Fit side-chains REVERT: A 252 LEU cc_start: 0.8504 (mt) cc_final: 0.8300 (mt) REVERT: A 253 LEU cc_start: 0.6450 (mt) cc_final: 0.6196 (mt) REVERT: A 288 ARG cc_start: 0.7640 (ptm160) cc_final: 0.7156 (ptm-80) REVERT: A 639 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7640 (mp) REVERT: A 651 VAL cc_start: 0.7039 (OUTLIER) cc_final: 0.6799 (p) REVERT: A 668 PHE cc_start: 0.7569 (t80) cc_final: 0.7221 (t80) REVERT: A 672 MET cc_start: 0.6866 (ttm) cc_final: 0.6496 (tmm) REVERT: A 697 MET cc_start: 0.6079 (mtp) cc_final: 0.5252 (mtp) REVERT: A 701 MET cc_start: 0.7049 (mmt) cc_final: 0.6747 (mmm) REVERT: B 253 LEU cc_start: 0.6595 (mt) cc_final: 0.6352 (mt) REVERT: B 486 MET cc_start: 0.8077 (ptm) cc_final: 0.7803 (ptt) REVERT: B 639 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7658 (mp) REVERT: B 672 MET cc_start: 0.7449 (tmm) cc_final: 0.6782 (tmm) REVERT: B 685 LEU cc_start: 0.7909 (tp) cc_final: 0.7560 (tp) outliers start: 36 outliers final: 28 residues processed: 156 average time/residue: 0.0988 time to fit residues: 23.3456 Evaluate side-chains 151 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.171274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142126 restraints weight = 19982.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140982 restraints weight = 14365.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141758 restraints weight = 15587.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142898 restraints weight = 9954.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144103 restraints weight = 8511.644| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12320 Z= 0.113 Angle : 0.539 11.006 16704 Z= 0.280 Chirality : 0.043 0.175 1894 Planarity : 0.004 0.041 2158 Dihedral : 4.810 59.648 1652 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 2.50 % Allowed : 21.40 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1514 helix: 1.87 (0.19), residues: 768 sheet: 0.26 (0.41), residues: 182 loop : -0.70 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 391 TYR 0.014 0.001 TYR B 188 PHE 0.024 0.001 PHE A 770 TRP 0.012 0.001 TRP A 43 HIS 0.003 0.000 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00248 (12320) covalent geometry : angle 0.53907 (16704) hydrogen bonds : bond 0.03886 ( 669) hydrogen bonds : angle 3.98134 ( 2058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.446 Fit side-chains REVERT: A 253 LEU cc_start: 0.6438 (mt) cc_final: 0.6183 (mt) REVERT: A 288 ARG cc_start: 0.7599 (ptm160) cc_final: 0.7176 (ptm-80) REVERT: A 639 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 651 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6707 (p) REVERT: A 668 PHE cc_start: 0.7545 (t80) cc_final: 0.7178 (t80) REVERT: A 672 MET cc_start: 0.7044 (ttm) cc_final: 0.6489 (tmm) REVERT: A 697 MET cc_start: 0.6135 (mtp) cc_final: 0.5716 (mtp) REVERT: B 252 LEU cc_start: 0.8557 (mt) cc_final: 0.8307 (mt) REVERT: B 253 LEU cc_start: 0.6579 (mt) cc_final: 0.6343 (mt) REVERT: B 486 MET cc_start: 0.8053 (ptm) cc_final: 0.7784 (ptt) REVERT: B 639 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 672 MET cc_start: 0.7438 (tmm) cc_final: 0.6729 (tmm) REVERT: B 685 LEU cc_start: 0.7851 (tp) cc_final: 0.7430 (tp) REVERT: B 796 ARG cc_start: 0.7245 (mpp80) cc_final: 0.6770 (mpp80) outliers start: 33 outliers final: 26 residues processed: 155 average time/residue: 0.0968 time to fit residues: 22.7051 Evaluate side-chains 157 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 544 HIS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.171275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142614 restraints weight = 20027.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.140866 restraints weight = 15551.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142122 restraints weight = 14846.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142713 restraints weight = 9141.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143344 restraints weight = 8246.539| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 12320 Z= 0.175 Angle : 0.823 59.198 16704 Z= 0.487 Chirality : 0.043 0.245 1894 Planarity : 0.004 0.041 2158 Dihedral : 4.842 59.622 1652 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 2.43 % Allowed : 21.55 % Favored : 76.02 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1514 helix: 1.88 (0.19), residues: 766 sheet: 0.27 (0.41), residues: 182 loop : -0.69 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 391 TYR 0.014 0.001 TYR B 188 PHE 0.018 0.001 PHE A 770 TRP 0.011 0.001 TRP A 43 HIS 0.003 0.000 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00317 (12320) covalent geometry : angle 0.82287 (16704) hydrogen bonds : bond 0.03890 ( 669) hydrogen bonds : angle 3.97832 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.03 seconds wall clock time: 31 minutes 23.42 seconds (1883.42 seconds total)