Starting phenix.real_space_refine on Fri Feb 6 04:35:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzq_72076/02_2026/9pzq_72076.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzq_72076/02_2026/9pzq_72076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pzq_72076/02_2026/9pzq_72076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzq_72076/02_2026/9pzq_72076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pzq_72076/02_2026/9pzq_72076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzq_72076/02_2026/9pzq_72076.map" } resolution = 4.07 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= 0.000 sd= 0.017 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 108 5.16 5 C 13931 2.51 5 N 3760 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21983 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'CIS': 3, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "G" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1005 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'CIS': 2, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 201 Planarities with less than four sites: {'UNK:plan-1': 201} Unresolved non-hydrogen planarities: 201 Chain: "A" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 4919 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 1 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 16, 'GLN:plan1': 4, 'GLU:plan': 13, 'TRP:plan': 1, 'ASP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 210 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 4906 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 24, 'TRANS': 616} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 10, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5123 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 8, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 4980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4980 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 24, 'TRANS': 617} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 5.25, per 1000 atoms: 0.24 Number of scatterers: 21983 At special positions: 0 Unit cell: (195.672, 138.864, 132.552, 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 108 16.00 O 4184 8.00 N 3760 7.00 C 13931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 800 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 36 sheets defined 37.4% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.965A pdb=" N UNK F 160 " --> pdb=" O UNK F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'G' and resid 105 through 109 Processing helix chain 'G' and resid 149 through 155 Processing helix chain 'G' and resid 211 through 216 Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'A' and resid 35 through 50 removed outlier: 4.123A pdb=" N ASN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.756A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.665A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.566A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 185 removed outlier: 4.487A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.552A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.538A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.516A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.914A pdb=" N ALA A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 665 through 668 removed outlier: 3.948A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.662A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.623A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 705 through 709 removed outlier: 3.535A pdb=" N LYS A 708 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.507A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 769 through 782 removed outlier: 3.571A pdb=" N ASN A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.801A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.779A pdb=" N ALA B 131 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 214 through 221 removed outlier: 3.670A pdb=" N GLN B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.862A pdb=" N VAL B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 3.653A pdb=" N ARG B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 removed outlier: 4.270A pdb=" N GLN B 336 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 337 " --> pdb=" O LEU B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 337' Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.670A pdb=" N ASP B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 removed outlier: 3.681A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.654A pdb=" N GLN B 671 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.565A pdb=" N ARG B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 707 removed outlier: 4.327A pdb=" N ARG B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.566A pdb=" N ARG B 741 " --> pdb=" O TYR B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 784 removed outlier: 4.656A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.903A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.533A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.554A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 188 removed outlier: 4.075A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 251 through 255 removed outlier: 4.003A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.610A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.841A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.627A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.555A pdb=" N SER C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.799A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 668 removed outlier: 4.239A pdb=" N ASN C 668 " --> pdb=" O THR C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 665 through 668' Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.500A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.773A pdb=" N GLU C 707 " --> pdb=" O TYR C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.611A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 769 through 782 removed outlier: 3.511A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.642A pdb=" N SER D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.776A pdb=" N GLN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.662A pdb=" N MET D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 180 through 193 Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.696A pdb=" N GLN D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.886A pdb=" N LEU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 308 Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 494 through 501 removed outlier: 3.532A pdb=" N GLY D 498 " --> pdb=" O ASN D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 522 Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 698 through 707 removed outlier: 4.219A pdb=" N ARG D 707 " --> pdb=" O GLN D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 722 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 771 through 784 Processing helix chain 'D' and resid 786 through 796 Processing sheet with id=AA1, first strand: chain 'F' and resid 23 through 26 Processing sheet with id=AA2, first strand: chain 'F' and resid 30 through 32 removed outlier: 6.496A pdb=" N UNK F 30 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK F 69 " --> pdb=" O UNK F 56 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N UNK F 58 " --> pdb=" O UNK F 67 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N UNK F 67 " --> pdb=" O UNK F 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 30 through 32 removed outlier: 6.496A pdb=" N UNK F 30 " --> pdb=" O UNK F 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 149 through 153 removed outlier: 5.199A pdb=" N UNK F 166 " --> pdb=" O UNK F 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N UNK F 212 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N UNK F 168 " --> pdb=" O UNK F 210 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N UNK F 210 " --> pdb=" O UNK F 168 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N UNK F 170 " --> pdb=" O UNK F 208 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N UNK F 208 " --> pdb=" O UNK F 170 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N UNK F 172 " --> pdb=" O UNK F 206 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N UNK F 206 " --> pdb=" O UNK F 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 149 through 153 removed outlier: 5.199A pdb=" N UNK F 166 " --> pdb=" O UNK F 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N UNK F 212 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N UNK F 168 " --> pdb=" O UNK F 210 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N UNK F 210 " --> pdb=" O UNK F 168 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N UNK F 170 " --> pdb=" O UNK F 208 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N UNK F 208 " --> pdb=" O UNK F 170 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N UNK F 172 " --> pdb=" O UNK F 206 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N UNK F 206 " --> pdb=" O UNK F 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AA8, first strand: chain 'G' and resid 30 through 34 removed outlier: 6.399A pdb=" N UNK G 31 " --> pdb=" O UNK G 133 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N UNK G 135 " --> pdb=" O UNK G 31 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N UNK G 33 " --> pdb=" O UNK G 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N UNK G 110 " --> pdb=" O UNK G 132 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N UNK G 63 " --> pdb=" O UNK G 72 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N UNK G 72 " --> pdb=" O UNK G 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 142 through 146 removed outlier: 5.660A pdb=" N UNK G 201 " --> pdb=" O UNK G 166 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N UNK G 202 " --> pdb=" O UNK G 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 182 through 183 removed outlier: 4.194A pdb=" N UNK G 176 " --> pdb=" O UNK G 183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.174A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 164 through 167 removed outlier: 6.456A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 248 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 221 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.424A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 476 removed outlier: 8.181A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AB7, first strand: chain 'A' and resid 488 through 490 removed outlier: 4.180A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 74 removed outlier: 6.882A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU B 72 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET B 74 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU B 40 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 101 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 199 through 205 removed outlier: 9.529A pdb=" N PHE B 170 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 228 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 256 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 405 through 410 Processing sheet with id=AC3, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AC4, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AC5, first strand: chain 'B' and resid 533 through 536 removed outlier: 6.645A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 59 through 65 removed outlier: 6.187A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.415A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C 221 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.594A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 478 removed outlier: 6.475A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE C 754 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 538 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AD2, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AD3, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AD4, first strand: chain 'D' and resid 68 through 74 removed outlier: 6.909A pdb=" N ILE D 36 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 72 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL D 38 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N MET D 74 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU D 40 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 101 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU D 98 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 199 through 205 removed outlier: 9.361A pdb=" N PHE D 170 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL D 226 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 228 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 230 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE D 227 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D 279 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 365 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS D 374 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 474 through 479 removed outlier: 3.563A pdb=" N THR D 410 " --> pdb=" O TYR D 478 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 409 " --> pdb=" O MET D 507 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AD8, first strand: chain 'D' and resid 529 through 530 removed outlier: 4.078A pdb=" N VAL D 529 " --> pdb=" O TYR D 761 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 533 through 536 removed outlier: 6.657A pdb=" N GLY D 683 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ASP D 731 " --> pdb=" O GLY D 683 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2352 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: 4.30 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6695 1.34 - 1.46: 4228 1.46 - 1.58: 11317 1.58 - 1.70: 0 1.70 - 1.82: 178 Bond restraints: 22418 Sorted by residual: bond pdb=" N VAL D 430 " pdb=" CA VAL D 430 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.91e+00 bond pdb=" N HIS A 67 " pdb=" CA HIS A 67 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.88e+00 bond pdb=" N THR A 66 " pdb=" CA THR A 66 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.71e+00 bond pdb=" C PRO C 95 " pdb=" N PRO C 96 " ideal model delta sigma weight residual 1.339 1.427 -0.088 3.40e-02 8.65e+02 6.65e+00 bond pdb=" C UNK G 168 " pdb=" N UNK G 169 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.40e-02 5.10e+03 6.50e+00 ... (remaining 22413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 29889 2.33 - 4.66: 636 4.66 - 6.98: 37 6.98 - 9.31: 16 9.31 - 11.64: 2 Bond angle restraints: 30580 Sorted by residual: angle pdb=" N UNK F 178 " pdb=" CA UNK F 178 " pdb=" CB UNK F 178 " ideal model delta sigma weight residual 110.50 101.49 9.01 1.70e+00 3.46e-01 2.81e+01 angle pdb=" N UNK F 176 " pdb=" CA UNK F 176 " pdb=" CB UNK F 176 " ideal model delta sigma weight residual 110.50 103.42 7.08 1.70e+00 3.46e-01 1.74e+01 angle pdb=" CA VAL B 430 " pdb=" C VAL B 430 " pdb=" O VAL B 430 " ideal model delta sigma weight residual 121.97 118.19 3.78 9.80e-01 1.04e+00 1.49e+01 angle pdb=" N THR A 105 " pdb=" CA THR A 105 " pdb=" C THR A 105 " ideal model delta sigma weight residual 113.45 118.59 -5.14 1.39e+00 5.18e-01 1.37e+01 angle pdb=" C THR A 442 " pdb=" N SER A 443 " pdb=" CA SER A 443 " ideal model delta sigma weight residual 120.09 124.64 -4.55 1.25e+00 6.40e-01 1.33e+01 ... (remaining 30575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 12877 15.17 - 30.34: 348 30.34 - 45.52: 73 45.52 - 60.69: 2 60.69 - 75.86: 9 Dihedral angle restraints: 13309 sinusoidal: 4561 harmonic: 8748 Sorted by residual: dihedral pdb=" CA UNK G 209 " pdb=" C UNK G 209 " pdb=" N UNK G 210 " pdb=" CA UNK G 210 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA UNK G 113 " pdb=" C UNK G 113 " pdb=" N UNK G 114 " pdb=" CA UNK G 114 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA UNK F 112 " pdb=" C UNK F 112 " pdb=" N UNK F 113 " pdb=" CA UNK F 113 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 13306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2647 0.046 - 0.092: 687 0.092 - 0.138: 232 0.138 - 0.185: 25 0.185 - 0.231: 5 Chirality restraints: 3596 Sorted by residual: chirality pdb=" CA UNK F 176 " pdb=" N UNK F 176 " pdb=" C UNK F 176 " pdb=" CB UNK F 176 " both_signs ideal model delta sigma weight residual False 2.52 2.75 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 755 " pdb=" CA ILE B 755 " pdb=" CG1 ILE B 755 " pdb=" CG2 ILE B 755 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE D 755 " pdb=" CA ILE D 755 " pdb=" CG1 ILE D 755 " pdb=" CG2 ILE D 755 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3593 not shown) Planarity restraints: 3963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " -0.049 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO A 104 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 103 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO C 104 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 94 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 95 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.038 5.00e-02 4.00e+02 ... (remaining 3960 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 276 2.66 - 3.22: 19270 3.22 - 3.78: 32368 3.78 - 4.34: 43095 4.34 - 4.90: 69299 Nonbonded interactions: 164308 Sorted by model distance: nonbonded pdb=" OD1 ASP D 421 " pdb=" NZ LYS D 454 " model vdw 2.097 3.120 nonbonded pdb=" OD1 ASP B 421 " pdb=" NZ LYS B 454 " model vdw 2.105 3.120 nonbonded pdb=" O GLN C 48 " pdb=" NH1 ARG C 52 " model vdw 2.121 3.120 nonbonded pdb=" NH1 ARG B 773 " pdb=" OE2 GLU C 528 " model vdw 2.135 3.120 nonbonded pdb=" O GLN A 48 " pdb=" NH1 ARG A 52 " model vdw 2.146 3.120 ... (remaining 164303 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 25 through 347 or (resid 348 through 349 and (name N or na \ me CA or name C or name O or name CB )) or resid 350 through 496 or (resid 497 a \ nd (name N or name CA or name C or name O or name CB )) or resid 498 through 676 \ or (resid 677 through 678 and (name N or name CA or name C or name O or name CB \ )) or resid 679 through 721 or (resid 722 and (name N or name CA or name C or n \ ame O or name CB )) or resid 723 through 789 or (resid 790 and (name N or name C \ A or name C or name O or name CB )) or resid 791 through 793 or (resid 794 and ( \ name N or name CA or name C or name O or name CB )) or resid 795 through 797)) selection = (chain 'C' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 35 or (resid 36 through 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 39 or (resid 40 through 41 and (n \ ame N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 thro \ ugh 45 and (name N or name CA or name C or name O or name CB )) or resid 46 thro \ ugh 47 or (resid 48 through 49 and (name N or name CA or name C or name O or nam \ e CB )) or resid 50 or (resid 51 and (name N or name CA or name C or name O or n \ ame CB )) or resid 52 through 54 or (resid 55 through 57 and (name N or name CA \ or name C or name O or name CB )) or resid 58 through 71 or (resid 72 and (name \ N or name CA or name C or name O or name CB )) or resid 73 through 99 or (resid \ 100 through 102 and (name N or name CA or name C or name O or name CB )) or resi \ d 103 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 173 or (resid 174 through 176 and (name N or name \ CA or name C or name O or name CB )) or resid 177 or (resid 178 and (name N or n \ ame CA or name C or name O or name CB )) or resid 179 through 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 20 \ 9 or (resid 210 through 211 and (name N or name CA or name C or name O or name C \ B )) or resid 212 or (resid 213 and (name N or name CA or name C or name O or na \ me CB )) or resid 214 through 224 or (resid 225 and (name N or name CA or name C \ or name O or name CB )) or resid 226 through 232 or (resid 233 through 237 and \ (name N or name CA or name C or name O or name CB )) or resid 238 through 250 or \ (resid 251 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 2 through 256 or (resid 257 through 258 and (name N or name CA or name C or name \ O or name CB )) or resid 259 or (resid 260 through 262 and (name N or name CA o \ r name C or name O or name CB )) or resid 263 or (resid 264 and (name N or name \ CA or name C or name O or name CB )) or resid 265 through 269 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 274 or \ (resid 275 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 6 through 297 or (resid 298 through 299 and (name N or name CA or name C or name \ O or name CB )) or resid 300 through 305 or (resid 306 and (name N or name CA o \ r name C or name O or name CB )) or resid 307 through 312 or (resid 313 and (nam \ e N or name CA or name C or name O or name CB )) or resid 314 through 315 or (re \ sid 316 and (name N or name CA or name C or name O or name CB )) or resid 317 th \ rough 321 or (resid 322 through 323 and (name N or name CA or name C or name O o \ r name CB )) or resid 324 through 336 or (resid 337 and (name N or name CA or na \ me C or name O or name CB )) or resid 338 or (resid 339 and (name N or name CA o \ r name C or name O or name CB )) or resid 340 through 341 or (resid 342 and (nam \ e N or name CA or name C or name O or name CB )) or resid 343 through 356 or (re \ sid 357 through 360 and (name N or name CA or name C or name O or name CB )) or \ resid 361 through 375 or (resid 376 through 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 416 or (resid 417 and (name N or n \ ame CA or name C or name O or name CB )) or resid 418 through 420 or (resid 421 \ and (name N or name CA or name C or name O or name CB )) or resid 422 or (resid \ 423 and (name N or name CA or name C or name O or name CB )) or resid 424 throug \ h 426 or (resid 427 and (name N or name CA or name C or name O or name CB )) or \ resid 428 through 673 or (resid 674 and (name N or name CA or name C or name O o \ r name CB )) or resid 675 through 694 or (resid 695 and (name N or name CA or na \ me C or name O or name CB )) or resid 696 through 697 or (resid 698 and (name N \ or name CA or name C or name O or name CB )) or resid 699 through 797)) } ncs_group { reference = (chain 'B' and (resid 34 through 201 or (resid 202 and (name N or name CA or nam \ e C or name O or name CB )) or resid 203 through 213 or (resid 214 and (name N o \ r name CA or name C or name O or name CB )) or resid 215 through 391 or (resid 3 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 393 through \ 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) or r \ esid 399 through 419 or (resid 420 and (name N or name CA or name C or name O or \ name CB )) or resid 421 through 674 or (resid 675 through 677 and (name N or na \ me CA or name C or name O or name CB )) or resid 678 through 753 or (resid 754 a \ nd (name N or name CA or name C or name O or name CB )) or resid 755 through 780 \ or (resid 781 and (name N or name CA or name C or name O or name CB )) or resid \ 782 through 800)) selection = (chain 'D' and (resid 34 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 54 or (resid 55 and ( \ name N or name CA or name C or name O or name CB )) or resid 56 through 62 or (r \ esid 63 and (name N or name CA or name C or name O or name CB )) or resid 64 thr \ ough 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or \ resid 77 through 93 or (resid 94 and (name N or name CA or name C or name O or \ name CB )) or resid 95 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 180 or (resid 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 90 or (resid 291 and (name N or name CA or name C or name O or name CB )) or res \ id 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or \ resid 294 through 307 or (resid 308 and (name N or name CA or name C or name O \ or name CB )) or resid 309 through 314 or (resid 315 through 316 and (name N or \ name CA or name C or name O or name CB )) or resid 317 through 320 or (resid 321 \ and (name N or name CA or name C or name O or name CB )) or resid 322 or resid \ 330 through 345 or (resid 346 and (name N or name CA or name C or name O or name \ CB )) or resid 347 through 351 or (resid 352 through 353 and (name N or name CA \ or name C or name O or name CB )) or resid 354 through 380 or (resid 381 and (n \ ame N or name CA or name C or name O or name CB )) or resid 382 through 449 or ( \ resid 450 and (name N or name CA or name C or name O or name CB )) or resid 451 \ through 456 or (resid 457 and (name N or name CA or name C or name O or name CB \ )) or resid 458 through 464 or (resid 465 and (name N or name CA or name C or na \ me O or name CB )) or resid 466 through 723 or (resid 724 and (name N or name CA \ or name C or name O or name CB )) or resid 725 through 800)) } ncs_group { reference = (chain 'F' and resid 30 through 244) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.280 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2466 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 : 0.004 0.088 22427 Z= 0.221 Angle : 0.768 11.640 30598 Z= 0.420 Chirality : 0.047 0.231 3596 Planarity : 0.006 0.075 3963 Dihedral : 8.434 75.862 7610 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.09 % Allowed : 1.31 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.86 (0.13), residues: 2579 helix: -2.30 (0.12), residues: 877 sheet: -1.80 (0.25), residues: 401 loop : -3.03 (0.14), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 681 TYR 0.018 0.002 TYR D 180 PHE 0.022 0.002 PHE D 183 TRP 0.021 0.002 TRP A 315 HIS 0.012 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00404 (22418) covalent geometry : angle 0.76807 (30580) SS BOND : bond 0.00101 ( 9) SS BOND : angle 0.84349 ( 18) hydrogen bonds : bond 0.14740 ( 825) hydrogen bonds : angle 7.37617 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: -0.1196 (mmm) cc_final: -0.1668 (mmm) REVERT: A 345 ASP cc_start: 0.3763 (m-30) cc_final: 0.3444 (m-30) REVERT: A 354 MET cc_start: -0.4064 (mmm) cc_final: -0.4616 (ptp) REVERT: B 135 MET cc_start: -0.2265 (ppp) cc_final: -0.3232 (ptp) REVERT: B 413 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6714 (tp30) REVERT: C 137 PHE cc_start: -0.0948 (t80) cc_final: -0.3571 (t80) REVERT: C 431 VAL cc_start: 0.5922 (t) cc_final: 0.5080 (m) REVERT: D 705 MET cc_start: -0.6881 (tmm) cc_final: -0.7419 (tmm) outliers start: 2 outliers final: 0 residues processed: 349 average time/residue: 0.1757 time to fit residues: 91.9447 Evaluate side-chains 204 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 293 HIS A 371 HIS A 449 HIS A 742 GLN A 770 GLN B 85 HIS ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 387 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN B 693 ASN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 147 GLN C 293 HIS C 311 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 HIS ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 GLN ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS D 358 HIS D 387 HIS D 482 ASN ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 ASN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.098085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.081460 restraints weight = 191094.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.081640 restraints weight = 144376.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.082587 restraints weight = 111372.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.082896 restraints weight = 75914.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.083169 restraints weight = 67441.324| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4320 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.175 22427 Z= 0.357 Angle : 1.081 14.203 30598 Z= 0.576 Chirality : 0.057 0.389 3596 Planarity : 0.009 0.200 3963 Dihedral : 7.039 32.315 3161 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 29.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.14 % Favored : 91.82 % Rotamer: Outliers : 0.33 % Allowed : 3.52 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.51 (0.14), residues: 2579 helix: -1.82 (0.14), residues: 897 sheet: -2.21 (0.27), residues: 321 loop : -2.77 (0.14), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 115 TYR 0.040 0.004 TYR A 526 PHE 0.054 0.005 PHE C 729 TRP 0.065 0.005 TRP C 731 HIS 0.017 0.003 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00754 (22418) covalent geometry : angle 1.08024 (30580) SS BOND : bond 0.00505 ( 9) SS BOND : angle 1.48348 ( 18) hydrogen bonds : bond 0.06032 ( 825) hydrogen bonds : angle 7.37242 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 264 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3158 (mmm) cc_final: 0.2006 (mmm) REVERT: A 155 MET cc_start: 0.5372 (mmp) cc_final: 0.5098 (mmm) REVERT: A 180 LEU cc_start: 0.9263 (tt) cc_final: 0.9036 (pp) REVERT: A 197 PHE cc_start: 0.8577 (t80) cc_final: 0.8268 (t80) REVERT: A 354 MET cc_start: -0.2966 (mmm) cc_final: -0.3458 (ptp) REVERT: A 484 PHE cc_start: 0.4578 (OUTLIER) cc_final: 0.3028 (m-10) REVERT: A 762 MET cc_start: 0.4100 (ttt) cc_final: 0.3785 (tmm) REVERT: A 769 LYS cc_start: 0.2729 (OUTLIER) cc_final: 0.2394 (tppt) REVERT: B 135 MET cc_start: -0.1697 (ppp) cc_final: -0.2330 (ptp) REVERT: B 158 MET cc_start: 0.5758 (tmm) cc_final: 0.5446 (tpt) REVERT: B 242 GLU cc_start: 0.3522 (tp30) cc_final: 0.3271 (tt0) REVERT: C 481 ASP cc_start: 0.1943 (p0) cc_final: 0.1618 (p0) REVERT: C 762 MET cc_start: 0.3795 (mmp) cc_final: 0.1003 (ttt) REVERT: D 85 HIS cc_start: 0.7726 (m-70) cc_final: 0.7266 (m-70) REVERT: D 177 PHE cc_start: 0.5295 (t80) cc_final: 0.4573 (t80) REVERT: D 380 ASN cc_start: 0.7779 (p0) cc_final: 0.7228 (p0) REVERT: D 442 ILE cc_start: 0.8007 (mm) cc_final: 0.7616 (mm) REVERT: D 496 MET cc_start: 0.2945 (ptm) cc_final: 0.2344 (ptm) REVERT: D 536 MET cc_start: 0.3188 (mmp) cc_final: 0.2977 (mmp) REVERT: D 705 MET cc_start: -0.4974 (tmm) cc_final: -0.5356 (tmm) REVERT: D 779 LEU cc_start: 0.5290 (mt) cc_final: 0.4876 (mt) REVERT: D 783 VAL cc_start: 0.6575 (t) cc_final: 0.6120 (t) outliers start: 7 outliers final: 1 residues processed: 270 average time/residue: 0.1600 time to fit residues: 67.2489 Evaluate side-chains 191 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 87 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 289 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 263 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 ASN B 146 GLN B 451 ASN B 482 ASN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS C 405 GLN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 146 GLN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 ASN ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.097869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.080595 restraints weight = 197630.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.081258 restraints weight = 148451.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.081562 restraints weight = 117742.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.082275 restraints weight = 98199.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.082530 restraints weight = 82759.231| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4149 moved from start: 0.8079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22427 Z= 0.161 Angle : 0.645 13.766 30598 Z= 0.337 Chirality : 0.044 0.217 3596 Planarity : 0.005 0.080 3963 Dihedral : 5.441 23.541 3161 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.15), residues: 2579 helix: -0.73 (0.16), residues: 896 sheet: -2.02 (0.27), residues: 341 loop : -2.41 (0.15), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 179 TYR 0.020 0.002 TYR D 312 PHE 0.030 0.002 PHE C 738 TRP 0.025 0.002 TRP D 795 HIS 0.007 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00353 (22418) covalent geometry : angle 0.64486 (30580) SS BOND : bond 0.00648 ( 9) SS BOND : angle 0.74459 ( 18) hydrogen bonds : bond 0.03466 ( 825) hydrogen bonds : angle 5.85666 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3968 (mmm) cc_final: 0.3373 (mmm) REVERT: A 501 MET cc_start: 0.2514 (ptt) cc_final: 0.1186 (mmt) REVERT: A 696 GLN cc_start: 0.5316 (mt0) cc_final: 0.5019 (mm-40) REVERT: B 135 MET cc_start: -0.0014 (ppp) cc_final: -0.1785 (ptp) REVERT: B 306 MET cc_start: 0.5869 (mtp) cc_final: 0.5382 (mtt) REVERT: C 174 ARG cc_start: 0.7900 (tpm170) cc_final: 0.7630 (tpm170) REVERT: C 358 ASN cc_start: 0.6411 (p0) cc_final: 0.5701 (p0) REVERT: C 394 MET cc_start: 0.2607 (mpp) cc_final: 0.1804 (mtp) REVERT: C 762 MET cc_start: 0.2916 (mmp) cc_final: 0.0553 (ttt) REVERT: D 85 HIS cc_start: 0.7270 (m-70) cc_final: 0.7037 (m-70) REVERT: D 200 MET cc_start: 0.4230 (ptt) cc_final: 0.2386 (ttm) REVERT: D 380 ASN cc_start: 0.7550 (p0) cc_final: 0.7311 (p0) REVERT: D 496 MET cc_start: 0.4137 (ptm) cc_final: 0.3218 (ptm) REVERT: D 536 MET cc_start: 0.2067 (mmp) cc_final: 0.1631 (tpp) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.1448 time to fit residues: 52.5081 Evaluate side-chains 170 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 227 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 294 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 29 optimal weight: 40.0000 chunk 136 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 146 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN C 196 GLN C 477 HIS ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.088891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.073383 restraints weight = 185259.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.073728 restraints weight = 144188.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.074489 restraints weight = 118452.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.073979 restraints weight = 103174.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.074146 restraints weight = 88327.863| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 1.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.232 22427 Z= 0.381 Angle : 1.155 20.428 30598 Z= 0.611 Chirality : 0.061 0.413 3596 Planarity : 0.009 0.131 3963 Dihedral : 7.836 43.545 3161 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 41.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.05 % Favored : 88.87 % Rotamer: Outliers : 0.75 % Allowed : 6.53 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.74 (0.14), residues: 2579 helix: -2.05 (0.14), residues: 867 sheet: -2.16 (0.28), residues: 308 loop : -2.92 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 115 TYR 0.047 0.004 TYR C 474 PHE 0.070 0.006 PHE B 183 TRP 0.056 0.004 TRP C 247 HIS 0.015 0.003 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00869 (22418) covalent geometry : angle 1.15435 (30580) SS BOND : bond 0.00744 ( 9) SS BOND : angle 1.64344 ( 18) hydrogen bonds : bond 0.06897 ( 825) hydrogen bonds : angle 8.07521 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.8790 (t80) cc_final: 0.8102 (t80) REVERT: A 326 MET cc_start: 0.5672 (mmp) cc_final: 0.4936 (mmt) REVERT: A 781 GLU cc_start: 0.0121 (OUTLIER) cc_final: -0.0338 (tm-30) REVERT: B 113 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7296 (pp) REVERT: B 135 MET cc_start: 0.0455 (ppp) cc_final: -0.2024 (mtm) REVERT: B 176 ILE cc_start: 0.1674 (OUTLIER) cc_final: 0.1187 (mp) REVERT: B 306 MET cc_start: 0.6488 (mtp) cc_final: 0.5961 (mtt) REVERT: B 701 MET cc_start: 0.6063 (mmm) cc_final: 0.5516 (mmm) REVERT: C 470 MET cc_start: 0.5466 (mmt) cc_final: 0.5178 (mmt) REVERT: C 762 MET cc_start: 0.3545 (mmp) cc_final: 0.0725 (ttp) REVERT: C 763 ARG cc_start: 0.2514 (OUTLIER) cc_final: 0.1973 (mtp180) REVERT: C 785 MET cc_start: 0.8107 (ppp) cc_final: 0.7780 (pmm) REVERT: D 186 PHE cc_start: 0.6718 (t80) cc_final: 0.5956 (t80) REVERT: D 200 MET cc_start: 0.5367 (ptt) cc_final: 0.4437 (ttm) REVERT: D 369 ASP cc_start: 0.8140 (m-30) cc_final: 0.7930 (m-30) REVERT: D 475 TYR cc_start: 0.4978 (p90) cc_final: 0.4508 (p90) REVERT: D 536 MET cc_start: 0.2881 (mmp) cc_final: 0.2240 (tpp) REVERT: D 709 ASN cc_start: 0.3524 (OUTLIER) cc_final: 0.2854 (m110) outliers start: 16 outliers final: 2 residues processed: 257 average time/residue: 0.1554 time to fit residues: 62.7761 Evaluate side-chains 189 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 113 optimal weight: 0.7980 chunk 243 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 39 optimal weight: 30.0000 chunk 78 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 146 GLN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN C 196 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 710 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 = 0.4339 r_free = 0.4339 target = 0.091535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.076674 restraints weight = 183849.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.077426 restraints weight = 141211.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.077918 restraints weight = 113431.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.078514 restraints weight = 97043.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.078772 restraints weight = 82946.012| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 1.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22427 Z= 0.144 Angle : 0.682 17.307 30598 Z= 0.353 Chirality : 0.045 0.243 3596 Planarity : 0.005 0.082 3963 Dihedral : 5.967 29.179 3161 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.05 % Allowed : 2.02 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.90 (0.15), residues: 2579 helix: -1.02 (0.16), residues: 896 sheet: -2.22 (0.26), residues: 353 loop : -2.51 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 397 TYR 0.020 0.002 TYR A 144 PHE 0.024 0.002 PHE D 253 TRP 0.028 0.002 TRP D 255 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00317 (22418) covalent geometry : angle 0.68153 (30580) SS BOND : bond 0.00382 ( 9) SS BOND : angle 1.27861 ( 18) hydrogen bonds : bond 0.03890 ( 825) hydrogen bonds : angle 6.33022 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.8204 (t80) cc_final: 0.7775 (t80) REVERT: A 326 MET cc_start: 0.5229 (mmp) cc_final: 0.4798 (mmm) REVERT: A 415 MET cc_start: 0.5738 (mpp) cc_final: 0.5536 (mpp) REVERT: B 113 LEU cc_start: 0.7707 (mt) cc_final: 0.7385 (tt) REVERT: B 135 MET cc_start: 0.0635 (ppp) cc_final: -0.2162 (mtm) REVERT: B 271 GLU cc_start: 0.8304 (mp0) cc_final: 0.6969 (mm-30) REVERT: B 306 MET cc_start: 0.6304 (mtp) cc_final: 0.5841 (mtp) REVERT: B 338 MET cc_start: 0.4951 (mmm) cc_final: 0.4522 (mmt) REVERT: B 701 MET cc_start: 0.6332 (mmm) cc_final: 0.5503 (mmm) REVERT: B 767 LYS cc_start: 0.5662 (mttt) cc_final: 0.5321 (mmtt) REVERT: C 209 MET cc_start: 0.7661 (tpt) cc_final: 0.7211 (mmp) REVERT: C 470 MET cc_start: 0.5238 (mmt) cc_final: 0.4046 (mmm) REVERT: C 762 MET cc_start: 0.1888 (mmp) cc_final: 0.1252 (ptm) REVERT: D 52 ARG cc_start: 0.6737 (mpt-90) cc_final: 0.5886 (mtt-85) REVERT: D 85 HIS cc_start: 0.7653 (m-70) cc_final: 0.7441 (m-70) REVERT: D 158 MET cc_start: 0.2779 (ppp) cc_final: 0.2259 (tmm) REVERT: D 186 PHE cc_start: 0.6160 (t80) cc_final: 0.5888 (t80) REVERT: D 369 ASP cc_start: 0.8068 (m-30) cc_final: 0.7858 (m-30) REVERT: D 536 MET cc_start: 0.2585 (mmp) cc_final: 0.1739 (tpp) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.1644 time to fit residues: 61.3234 Evaluate side-chains 180 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 79 optimal weight: 0.1980 chunk 106 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 211 optimal weight: 0.0980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 766 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 HIS D 703 GLN ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.088936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.071993 restraints weight = 188961.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.072244 restraints weight = 154779.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.072636 restraints weight = 127381.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.073704 restraints weight = 103325.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.073541 restraints weight = 82519.171| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 1.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 22427 Z= 0.209 Angle : 0.790 13.902 30598 Z= 0.413 Chirality : 0.048 0.263 3596 Planarity : 0.006 0.071 3963 Dihedral : 6.144 28.897 3161 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.04 (0.15), residues: 2579 helix: -1.11 (0.16), residues: 917 sheet: -2.39 (0.25), residues: 375 loop : -2.60 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 390 TYR 0.030 0.003 TYR B 761 PHE 0.032 0.003 PHE C 472 TRP 0.022 0.003 TRP D 255 HIS 0.008 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00467 (22418) covalent geometry : angle 0.78921 (30580) SS BOND : bond 0.00499 ( 9) SS BOND : angle 1.42071 ( 18) hydrogen bonds : bond 0.04585 ( 825) hydrogen bonds : angle 6.51023 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.8515 (t80) cc_final: 0.7999 (t80) REVERT: A 326 MET cc_start: 0.6195 (mmp) cc_final: 0.5583 (mmm) REVERT: A 415 MET cc_start: 0.6019 (mpp) cc_final: 0.5754 (mpp) REVERT: B 112 MET cc_start: 0.5806 (ppp) cc_final: 0.5201 (ppp) REVERT: B 135 MET cc_start: 0.0460 (ppp) cc_final: -0.2155 (mtm) REVERT: B 200 MET cc_start: 0.2976 (tpt) cc_final: 0.1762 (tpt) REVERT: B 306 MET cc_start: 0.6457 (mtp) cc_final: 0.5830 (mtp) REVERT: B 338 MET cc_start: 0.6518 (mmm) cc_final: 0.5980 (mmt) REVERT: B 701 MET cc_start: 0.6584 (mmm) cc_final: 0.6328 (mmm) REVERT: C 501 MET cc_start: 0.2845 (tpp) cc_final: 0.2452 (mmm) REVERT: C 502 MET cc_start: 0.4049 (tpp) cc_final: 0.3646 (tpt) REVERT: C 762 MET cc_start: 0.3128 (mmp) cc_final: 0.1736 (ptm) REVERT: D 158 MET cc_start: 0.2552 (ppp) cc_final: 0.2330 (tmm) REVERT: D 338 MET cc_start: -0.3885 (mmt) cc_final: -0.4620 (mmp) REVERT: D 380 ASN cc_start: 0.8261 (p0) cc_final: 0.8013 (p0) REVERT: D 475 TYR cc_start: 0.3696 (p90) cc_final: 0.3324 (p90) REVERT: D 536 MET cc_start: 0.3571 (mmp) cc_final: 0.1958 (tpp) REVERT: D 779 LEU cc_start: 0.7116 (mt) cc_final: 0.6793 (mt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1531 time to fit residues: 54.1683 Evaluate side-chains 172 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 274 optimal weight: 3.9990 chunk 268 optimal weight: 0.0570 chunk 190 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 697 ASN D 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.090524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.077519 restraints weight = 196211.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.077985 restraints weight = 181776.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.078590 restraints weight = 132616.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.079083 restraints weight = 91926.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.079193 restraints weight = 75524.453| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5243 moved from start: 1.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 22427 Z= 0.131 Angle : 0.646 11.538 30598 Z= 0.334 Chirality : 0.044 0.210 3596 Planarity : 0.005 0.066 3963 Dihedral : 5.499 26.612 3161 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.51 (0.15), residues: 2579 helix: -0.55 (0.16), residues: 896 sheet: -2.00 (0.26), residues: 339 loop : -2.40 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 115 TYR 0.022 0.002 TYR D 312 PHE 0.023 0.002 PHE C 784 TRP 0.025 0.002 TRP C 315 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00294 (22418) covalent geometry : angle 0.64599 (30580) SS BOND : bond 0.00301 ( 9) SS BOND : angle 1.24130 ( 18) hydrogen bonds : bond 0.03704 ( 825) hydrogen bonds : angle 5.86996 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.5713 (mmp) cc_final: 0.5176 (mmm) REVERT: A 394 MET cc_start: 0.1134 (tpp) cc_final: -0.2253 (ptt) REVERT: A 501 MET cc_start: 0.6292 (mpp) cc_final: 0.4590 (tpp) REVERT: B 135 MET cc_start: 0.0705 (ppp) cc_final: -0.2110 (mtm) REVERT: B 200 MET cc_start: 0.2619 (tpt) cc_final: 0.1360 (tpt) REVERT: B 306 MET cc_start: 0.6258 (mtp) cc_final: 0.5865 (mtp) REVERT: B 338 MET cc_start: 0.6687 (mmm) cc_final: 0.6158 (mmt) REVERT: B 701 MET cc_start: 0.6807 (mmm) cc_final: 0.6433 (mmm) REVERT: C 762 MET cc_start: 0.2693 (mmp) cc_final: 0.1861 (ptm) REVERT: D 52 ARG cc_start: 0.6607 (mpt-90) cc_final: 0.5596 (mtt-85) REVERT: D 338 MET cc_start: -0.3997 (mmt) cc_final: -0.4391 (mmt) REVERT: D 380 ASN cc_start: 0.8032 (p0) cc_final: 0.7768 (p0) REVERT: D 535 VAL cc_start: 0.6779 (t) cc_final: 0.6188 (p) REVERT: D 536 MET cc_start: 0.3478 (mmp) cc_final: 0.2312 (tpp) REVERT: D 779 LEU cc_start: 0.7124 (mt) cc_final: 0.6655 (mt) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1456 time to fit residues: 52.1411 Evaluate side-chains 170 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 24 optimal weight: 40.0000 chunk 197 optimal weight: 0.0170 chunk 297 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 overall best weight: 3.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS D 687 ASN ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.086027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.071244 restraints weight = 181366.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.071781 restraints weight = 172884.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.071628 restraints weight = 121647.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.071596 restraints weight = 95327.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.071558 restraints weight = 91924.053| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 1.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 22427 Z= 0.261 Angle : 0.890 18.504 30598 Z= 0.466 Chirality : 0.051 0.327 3596 Planarity : 0.006 0.088 3963 Dihedral : 6.564 36.901 3161 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 31.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.97 % Favored : 88.99 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.04 (0.15), residues: 2579 helix: -1.14 (0.16), residues: 906 sheet: -2.31 (0.26), residues: 340 loop : -2.62 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 360 TYR 0.047 0.003 TYR B 355 PHE 0.035 0.004 PHE A 693 TRP 0.059 0.004 TRP D 255 HIS 0.009 0.002 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00561 (22418) covalent geometry : angle 0.88945 (30580) SS BOND : bond 0.00490 ( 9) SS BOND : angle 1.29756 ( 18) hydrogen bonds : bond 0.05198 ( 825) hydrogen bonds : angle 6.87203 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7591 (mp0) REVERT: A 394 MET cc_start: -0.0243 (tpp) cc_final: -0.2709 (ptt) REVERT: A 501 MET cc_start: 0.7194 (mpp) cc_final: 0.6992 (mpp) REVERT: B 112 MET cc_start: 0.7102 (ppp) cc_final: 0.6786 (ppp) REVERT: B 133 MET cc_start: 0.7617 (mmp) cc_final: 0.6970 (mmp) REVERT: B 135 MET cc_start: -0.0562 (ppp) cc_final: -0.2485 (mtm) REVERT: B 180 TYR cc_start: 0.6568 (p90) cc_final: 0.6307 (p90) REVERT: B 306 MET cc_start: 0.6042 (mtp) cc_final: 0.5648 (mtp) REVERT: B 338 MET cc_start: 0.6942 (mmm) cc_final: 0.6488 (mmt) REVERT: B 403 ASP cc_start: 0.7376 (m-30) cc_final: 0.7014 (t70) REVERT: B 496 MET cc_start: 0.8145 (mmm) cc_final: 0.7887 (mmm) REVERT: B 701 MET cc_start: 0.7002 (mmm) cc_final: 0.6553 (mmp) REVERT: C 762 MET cc_start: 0.3048 (mmp) cc_final: 0.0961 (ttt) REVERT: D 380 ASN cc_start: 0.8361 (p0) cc_final: 0.7952 (p0) REVERT: D 475 TYR cc_start: 0.3295 (p90) cc_final: 0.3017 (p90) REVERT: D 536 MET cc_start: 0.4076 (mmp) cc_final: 0.2854 (tpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1212 time to fit residues: 42.3350 Evaluate side-chains 152 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 77 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 218 GLN D 687 ASN ** D 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.082774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.068072 restraints weight = 179871.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.068694 restraints weight = 168065.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.068230 restraints weight = 121895.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.068124 restraints weight = 98611.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.068268 restraints weight = 98854.902| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 2.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 22427 Z= 0.327 Angle : 0.983 15.412 30598 Z= 0.524 Chirality : 0.055 0.385 3596 Planarity : 0.007 0.104 3963 Dihedral : 7.125 39.050 3161 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 33.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.43 (0.15), residues: 2579 helix: -1.60 (0.15), residues: 895 sheet: -2.54 (0.26), residues: 307 loop : -2.73 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 763 TYR 0.049 0.004 TYR A 410 PHE 0.062 0.004 PHE C 472 TRP 0.078 0.004 TRP C 151 HIS 0.013 0.002 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00677 (22418) covalent geometry : angle 0.98220 (30580) SS BOND : bond 0.00380 ( 9) SS BOND : angle 1.82730 ( 18) hydrogen bonds : bond 0.05993 ( 825) hydrogen bonds : angle 7.50038 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6328 (mpp) cc_final: 0.5394 (mpp) REVERT: A 387 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7797 (mp0) REVERT: A 394 MET cc_start: 0.0747 (tpp) cc_final: 0.0318 (tpt) REVERT: A 702 MET cc_start: 0.8378 (mpp) cc_final: 0.7927 (mpp) REVERT: B 112 MET cc_start: 0.7498 (ppp) cc_final: 0.7144 (ppp) REVERT: B 133 MET cc_start: 0.7714 (mmp) cc_final: 0.7371 (mmm) REVERT: B 135 MET cc_start: 0.1458 (ppp) cc_final: 0.1070 (ptp) REVERT: B 180 TYR cc_start: 0.6656 (p90) cc_final: 0.6058 (p90) REVERT: B 242 GLU cc_start: 0.7686 (tt0) cc_final: 0.7333 (tt0) REVERT: B 271 GLU cc_start: 0.8722 (mp0) cc_final: 0.8314 (mm-30) REVERT: B 306 MET cc_start: 0.6980 (mtp) cc_final: 0.6197 (mtp) REVERT: B 403 ASP cc_start: 0.8656 (m-30) cc_final: 0.8378 (m-30) REVERT: C 354 MET cc_start: 0.4549 (tpp) cc_final: 0.4179 (tpp) REVERT: C 762 MET cc_start: 0.3264 (mmp) cc_final: 0.1015 (ttp) REVERT: D 158 MET cc_start: 0.7681 (tmm) cc_final: 0.7434 (tmm) REVERT: D 380 ASN cc_start: 0.8483 (p0) cc_final: 0.7995 (p0) REVERT: D 535 VAL cc_start: 0.7262 (t) cc_final: 0.7025 (p) REVERT: D 536 MET cc_start: 0.5357 (mmp) cc_final: 0.4513 (tpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1462 time to fit residues: 44.2111 Evaluate side-chains 137 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 50.0000 chunk 254 optimal weight: 0.7980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS B 216 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.083472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.067769 restraints weight = 188451.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.067613 restraints weight = 160841.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.068240 restraints weight = 132044.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.068378 restraints weight = 104487.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.068476 restraints weight = 91789.534| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 2.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22427 Z= 0.198 Angle : 0.785 13.086 30598 Z= 0.408 Chirality : 0.048 0.222 3596 Planarity : 0.005 0.075 3963 Dihedral : 6.387 37.869 3161 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.00 (0.15), residues: 2579 helix: -1.16 (0.16), residues: 912 sheet: -2.29 (0.26), residues: 336 loop : -2.54 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 115 TYR 0.024 0.002 TYR C 128 PHE 0.031 0.003 PHE D 170 TRP 0.035 0.003 TRP C 151 HIS 0.010 0.002 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00440 (22418) covalent geometry : angle 0.78445 (30580) SS BOND : bond 0.00353 ( 9) SS BOND : angle 1.34154 ( 18) hydrogen bonds : bond 0.04751 ( 825) hydrogen bonds : angle 6.78583 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8244 (mpp) cc_final: 0.8020 (mpp) REVERT: A 354 MET cc_start: -0.2083 (mmp) cc_final: -0.2353 (mmp) REVERT: A 387 GLU cc_start: 0.8650 (mt-10) cc_final: 0.7998 (mp0) REVERT: A 394 MET cc_start: 0.0943 (tpp) cc_final: 0.0491 (tpt) REVERT: A 702 MET cc_start: 0.8492 (mpp) cc_final: 0.8206 (mpp) REVERT: A 724 ASN cc_start: 0.8025 (m-40) cc_final: 0.7823 (m-40) REVERT: B 133 MET cc_start: 0.7903 (mmp) cc_final: 0.7240 (mmp) REVERT: B 135 MET cc_start: 0.1669 (ppp) cc_final: 0.1000 (ptp) REVERT: B 158 MET cc_start: 0.8670 (mmp) cc_final: 0.8376 (mtt) REVERT: B 271 GLU cc_start: 0.8745 (mp0) cc_final: 0.8020 (mp0) REVERT: B 306 MET cc_start: 0.6671 (mtp) cc_final: 0.6130 (mtp) REVERT: B 312 TYR cc_start: 0.6552 (t80) cc_final: 0.6254 (t80) REVERT: B 701 MET cc_start: 0.8328 (mmm) cc_final: 0.7931 (mmm) REVERT: D 380 ASN cc_start: 0.8288 (p0) cc_final: 0.7863 (p0) REVERT: D 507 MET cc_start: 0.7172 (mpp) cc_final: 0.6169 (mpp) REVERT: D 522 VAL cc_start: 0.5943 (p) cc_final: 0.5625 (m) REVERT: D 536 MET cc_start: 0.6390 (mmp) cc_final: 0.5273 (tpp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1367 time to fit residues: 43.4979 Evaluate side-chains 139 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 224 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 280 optimal weight: 8.9990 chunk 35 optimal weight: 50.0000 chunk 196 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS ** D 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 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 = 0.4147 r_free = 0.4147 target = 0.080566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.065289 restraints weight = 182762.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.065448 restraints weight = 172323.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.065529 restraints weight = 123824.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.065472 restraints weight = 94075.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.065507 restraints weight = 89997.833| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 2.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 22427 Z= 0.260 Angle : 0.902 15.097 30598 Z= 0.473 Chirality : 0.052 0.511 3596 Planarity : 0.006 0.087 3963 Dihedral : 6.861 38.091 3161 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 31.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.17 (0.15), residues: 2579 helix: -1.36 (0.15), residues: 912 sheet: -2.31 (0.27), residues: 290 loop : -2.63 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 212 TYR 0.031 0.003 TYR A 535 PHE 0.044 0.004 PHE C 472 TRP 0.039 0.004 TRP C 151 HIS 0.013 0.002 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00580 (22418) covalent geometry : angle 0.90136 (30580) SS BOND : bond 0.00393 ( 9) SS BOND : angle 1.66264 ( 18) hydrogen bonds : bond 0.05251 ( 825) hydrogen bonds : angle 7.26002 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.19 seconds wall clock time: 71 minutes 37.63 seconds (4297.63 seconds total)