Starting phenix.real_space_refine on Fri Mar 6 03:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rza_24756/03_2026/7rza_24756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rza_24756/03_2026/7rza_24756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rza_24756/03_2026/7rza_24756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rza_24756/03_2026/7rza_24756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rza_24756/03_2026/7rza_24756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rza_24756/03_2026/7rza_24756.map" } resolution = 4.26 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= 0.002 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 144 5.16 5 C 17894 2.51 5 N 4618 2.21 5 O 5194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27850 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7713 Classifications: {'peptide': 981} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 952} Chain breaks: 3 Chain: "B" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6186 Classifications: {'peptide': 785} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 761} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 12.78, per 1000 atoms: 0.46 Number of scatterers: 27850 At special positions: 0 Unit cell: (122.01, 163.51, 185.92, 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 144 16.00 O 5194 8.00 N 4618 7.00 C 17894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.04 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6492 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 44 sheets defined 49.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.607A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.075A pdb=" N ILE A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.523A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.698A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.533A pdb=" N TYR A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.873A pdb=" N ILE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.697A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.260A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.605A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.682A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 4.111A pdb=" N GLU A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 470 removed outlier: 3.545A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.632A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 547 removed outlier: 3.540A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 585 removed outlier: 3.828A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 627 removed outlier: 3.624A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.537A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.588A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.560A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 770 removed outlier: 3.634A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 770 " --> pdb=" O TRP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 822 removed outlier: 3.697A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1029 removed outlier: 3.896A pdb=" N ALA A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1011 " --> pdb=" O GLY A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1147 removed outlier: 3.725A pdb=" N LEU A1127 " --> pdb=" O GLY A1123 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A1130 " --> pdb=" O TRP A1126 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A1145 " --> pdb=" O VAL A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1194 removed outlier: 3.572A pdb=" N ALA A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1167 " --> pdb=" O ASN A1163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A1185 " --> pdb=" O HIS A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1233 removed outlier: 3.745A pdb=" N MET A1221 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1222 " --> pdb=" O THR A1218 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A1223 " --> pdb=" O CYS A1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.707A pdb=" N ARG B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.865A pdb=" N ILE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.522A pdb=" N LEU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.705A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 4.014A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 4.039A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.625A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.539A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.578A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.652A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.612A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.745A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.682A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.914A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.706A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.509A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.740A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 675 " --> pdb=" O TRP B 671 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.505A pdb=" N LYS B 695 " --> pdb=" O ALA B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.988A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 712 " --> pdb=" O MET B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 743 through 756 removed outlier: 3.618A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.758A pdb=" N LYS B 765 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.995A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 removed outlier: 3.606A pdb=" N GLY C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 removed outlier: 4.074A pdb=" N ILE C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.523A pdb=" N ILE C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.698A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.533A pdb=" N TYR C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.874A pdb=" N ILE C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.697A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.259A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.605A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.682A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 4.111A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 470 removed outlier: 3.545A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.632A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 489 " --> pdb=" O ARG C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 547 removed outlier: 3.540A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 585 removed outlier: 3.827A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 627 removed outlier: 3.624A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.536A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.589A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.560A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 770 removed outlier: 3.634A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 770 " --> pdb=" O TRP C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.698A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1029 removed outlier: 3.896A pdb=" N ALA C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C1011 " --> pdb=" O GLY C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1147 removed outlier: 3.723A pdb=" N LEU C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C1130 " --> pdb=" O TRP C1126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C1145 " --> pdb=" O VAL C1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1194 removed outlier: 3.573A pdb=" N ALA C1166 " --> pdb=" O LEU C1162 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C1167 " --> pdb=" O ASN C1163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C1185 " --> pdb=" O HIS C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1233 removed outlier: 3.746A pdb=" N MET C1221 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C1222 " --> pdb=" O THR C1218 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C1223 " --> pdb=" O CYS C1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.706A pdb=" N ARG D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.866A pdb=" N ILE D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.524A pdb=" N LEU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 157 removed outlier: 3.706A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 4.015A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 removed outlier: 4.039A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.626A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.538A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.577A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.652A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.611A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.745A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.682A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.914A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.706A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.510A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.740A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 675 " --> pdb=" O TRP D 671 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 677 " --> pdb=" O TYR D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.505A pdb=" N LYS D 695 " --> pdb=" O ALA D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.987A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 743 through 756 removed outlier: 3.618A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 770 removed outlier: 3.757A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS D 770 " --> pdb=" O TRP D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 781 Processing helix chain 'D' and resid 792 through 820 removed outlier: 3.996A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.555A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 75 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.869A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 221 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 194 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR A 220 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.724A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.665A pdb=" N VAL A 381 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 399 Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.973A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 704 through 705 removed outlier: 4.169A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 646 through 648 removed outlier: 5.611A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1033 through 1039 removed outlier: 3.508A pdb=" N THR A1093 " --> pdb=" O CYS A1033 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.633A pdb=" N ILE B 12 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.633A pdb=" N ILE B 12 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ALA B 72 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLN B 13 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.375A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 245 through 246 removed outlier: 3.526A pdb=" N ARG B 369 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.823A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.790A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC2, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AC3, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.657A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 730 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.811A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.555A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 75 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.871A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 221 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 194 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 346 through 347 removed outlier: 3.723A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 363 Processing sheet with id=AC9, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.666A pdb=" N VAL C 381 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AD2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AD3, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.974A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 704 through 705 removed outlier: 4.169A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 646 through 648 removed outlier: 5.610A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 1033 through 1039 removed outlier: 3.508A pdb=" N THR C1093 " --> pdb=" O CYS C1033 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.633A pdb=" N ILE D 12 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.633A pdb=" N ILE D 12 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ALA D 72 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN D 13 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE D 74 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.375A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 245 through 246 removed outlier: 3.526A pdb=" N ARG D 369 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 346 through 347 removed outlier: 3.823A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.790A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AE7, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.656A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 730 " --> pdb=" O LEU D 498 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.812A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) 1203 hydrogen bonds defined for protein. 3525 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: 5.40 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8830 1.35 - 1.47: 7253 1.47 - 1.60: 12135 1.60 - 1.72: 4 1.72 - 1.85: 230 Bond restraints: 28452 Sorted by residual: bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.203 1.449 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.203 1.448 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C05 QUS A1401 " pdb=" O19 QUS A1401 " ideal model delta sigma weight residual 1.203 1.448 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C05 QUS C1401 " pdb=" O19 QUS C1401 " ideal model delta sigma weight residual 1.203 1.447 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C04 QUS D1301 " pdb=" O18 QUS D1301 " ideal model delta sigma weight residual 1.212 1.412 -0.200 2.00e-02 2.50e+03 9.97e+01 ... (remaining 28447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 37547 2.64 - 5.27: 793 5.27 - 7.91: 97 7.91 - 10.55: 21 10.55 - 13.18: 8 Bond angle restraints: 38466 Sorted by residual: angle pdb=" C SER C1153 " pdb=" N SER C1154 " pdb=" CA SER C1154 " ideal model delta sigma weight residual 120.79 128.78 -7.99 1.39e+00 5.18e-01 3.31e+01 angle pdb=" C SER A1153 " pdb=" N SER A1154 " pdb=" CA SER A1154 " ideal model delta sigma weight residual 120.79 128.73 -7.94 1.39e+00 5.18e-01 3.26e+01 angle pdb=" N LEU B 233 " pdb=" CA LEU B 233 " pdb=" C LEU B 233 " ideal model delta sigma weight residual 113.72 106.55 7.17 1.30e+00 5.92e-01 3.04e+01 angle pdb=" N LEU D 233 " pdb=" CA LEU D 233 " pdb=" C LEU D 233 " ideal model delta sigma weight residual 113.72 106.57 7.15 1.30e+00 5.92e-01 3.02e+01 angle pdb=" C GLY D 774 " pdb=" N ALA D 775 " pdb=" CA ALA D 775 " ideal model delta sigma weight residual 120.38 128.40 -8.02 1.46e+00 4.69e-01 3.02e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 15860 16.99 - 33.98: 748 33.98 - 50.97: 208 50.97 - 67.96: 22 67.96 - 84.96: 16 Dihedral angle restraints: 16854 sinusoidal: 6692 harmonic: 10162 Sorted by residual: dihedral pdb=" CA ASN B 318 " pdb=" C ASN B 318 " pdb=" N PRO B 319 " pdb=" CA PRO B 319 " ideal model delta harmonic sigma weight residual -180.00 -119.12 -60.88 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ASN D 318 " pdb=" C ASN D 318 " pdb=" N PRO D 319 " pdb=" CA PRO D 319 " ideal model delta harmonic sigma weight residual -180.00 -119.12 -60.88 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ASN C 318 " pdb=" C ASN C 318 " pdb=" N PRO C 319 " pdb=" CA PRO C 319 " ideal model delta harmonic sigma weight residual 180.00 -131.75 -48.25 0 5.00e+00 4.00e-02 9.31e+01 ... (remaining 16851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3211 0.054 - 0.109: 865 0.109 - 0.163: 168 0.163 - 0.218: 22 0.218 - 0.272: 8 Chirality restraints: 4274 Sorted by residual: chirality pdb=" CB VAL B 165 " pdb=" CA VAL B 165 " pdb=" CG1 VAL B 165 " pdb=" CG2 VAL B 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL D 165 " pdb=" CA VAL D 165 " pdb=" CG1 VAL D 165 " pdb=" CG2 VAL D 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 4271 not shown) Planarity restraints: 4850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO B 99 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO D 99 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO C 99 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.040 5.00e-02 4.00e+02 ... (remaining 4847 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6552 2.78 - 3.31: 25370 3.31 - 3.84: 44902 3.84 - 4.37: 52710 4.37 - 4.90: 88608 Nonbonded interactions: 218142 Sorted by model distance: nonbonded pdb=" OG SER B 729 " pdb=" OG SER C 729 " model vdw 2.247 3.040 nonbonded pdb=" O VAL A 681 " pdb=" OH TYR A 700 " model vdw 2.248 3.040 nonbonded pdb=" O VAL C 681 " pdb=" OH TYR C 700 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR C 655 " pdb=" O18 QUS C1401 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" O18 QUS A1401 " model vdw 2.263 3.040 ... (remaining 218137 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.150 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 28462 Z= 0.354 Angle : 0.995 13.181 38486 Z= 0.568 Chirality : 0.052 0.272 4274 Planarity : 0.006 0.076 4850 Dihedral : 11.491 84.955 10332 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.53 % Allowed : 5.69 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.18 % 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: -4.39 (0.11), residues: 3504 helix: -3.41 (0.07), residues: 1648 sheet: -2.54 (0.22), residues: 432 loop : -2.11 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 599 TYR 0.032 0.003 TYR A 218 PHE 0.030 0.003 PHE C 56 TRP 0.025 0.003 TRP A 374 HIS 0.012 0.003 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00738 (28452) covalent geometry : angle 0.99378 (38466) SS BOND : bond 0.00633 ( 10) SS BOND : angle 2.15771 ( 20) hydrogen bonds : bond 0.29111 ( 1199) hydrogen bonds : angle 9.10856 ( 3525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 849 time to evaluate : 0.996 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 79 LYS cc_start: 0.8977 (tptt) cc_final: 0.8770 (tppt) REVERT: A 95 SER cc_start: 0.8907 (m) cc_final: 0.8443 (p) REVERT: A 111 ILE cc_start: 0.8940 (mp) cc_final: 0.8569 (mm) REVERT: A 174 ASP cc_start: 0.5921 (p0) cc_final: 0.5652 (p0) REVERT: A 293 THR cc_start: 0.8233 (m) cc_final: 0.8031 (t) REVERT: A 359 ASN cc_start: 0.8053 (m-40) cc_final: 0.7712 (m-40) REVERT: A 373 TYR cc_start: 0.8180 (p90) cc_final: 0.7865 (p90) REVERT: A 393 LYS cc_start: 0.8632 (ttpm) cc_final: 0.8377 (ttmm) REVERT: A 435 HIS cc_start: 0.6893 (t-90) cc_final: 0.6671 (t-170) REVERT: A 527 MET cc_start: 0.7447 (mmp) cc_final: 0.7071 (mmm) REVERT: A 720 THR cc_start: 0.7631 (p) cc_final: 0.7277 (p) REVERT: A 766 TRP cc_start: 0.6540 (t-100) cc_final: 0.6044 (m100) REVERT: A 1088 LEU cc_start: 0.7289 (pp) cc_final: 0.6956 (mm) REVERT: A 1096 TRP cc_start: 0.6714 (m100) cc_final: 0.6487 (m-10) REVERT: B 185 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7068 (tp30) REVERT: B 296 PHE cc_start: 0.7563 (m-80) cc_final: 0.7264 (m-10) REVERT: B 358 ILE cc_start: 0.8563 (mt) cc_final: 0.8355 (mt) REVERT: B 503 MET cc_start: 0.7706 (ttp) cc_final: 0.7372 (tmm) REVERT: B 533 TYR cc_start: 0.7079 (t80) cc_final: 0.6873 (t80) REVERT: B 585 MET cc_start: 0.9176 (mmt) cc_final: 0.8927 (mmt) REVERT: B 612 ILE cc_start: 0.8883 (mm) cc_final: 0.8594 (tp) REVERT: B 619 ASN cc_start: 0.8130 (t0) cc_final: 0.7915 (t0) REVERT: B 667 PHE cc_start: 0.7349 (m-10) cc_final: 0.7067 (m-80) REVERT: C 140 ASP cc_start: 0.7847 (m-30) cc_final: 0.6937 (t0) REVERT: C 174 ASP cc_start: 0.5844 (p0) cc_final: 0.5639 (p0) REVERT: C 197 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6793 (tt0) REVERT: C 287 ASP cc_start: 0.7981 (m-30) cc_final: 0.7634 (m-30) REVERT: C 330 GLU cc_start: 0.8054 (pt0) cc_final: 0.7700 (pm20) REVERT: C 349 GLN cc_start: 0.7519 (pp30) cc_final: 0.7083 (pp30) REVERT: C 359 ASN cc_start: 0.8010 (m-40) cc_final: 0.7489 (m-40) REVERT: C 361 MET cc_start: 0.7111 (mtp) cc_final: 0.6896 (mtp) REVERT: C 427 ASP cc_start: 0.8115 (m-30) cc_final: 0.7591 (t70) REVERT: C 435 HIS cc_start: 0.7014 (t-90) cc_final: 0.6744 (t-170) REVERT: C 543 VAL cc_start: 0.8265 (t) cc_final: 0.8052 (p) REVERT: C 607 PHE cc_start: 0.8686 (t80) cc_final: 0.8446 (t80) REVERT: C 610 LEU cc_start: 0.9369 (tt) cc_final: 0.8965 (tp) REVERT: C 1186 GLN cc_start: 0.7913 (tt0) cc_final: 0.7605 (tt0) REVERT: C 1196 PRO cc_start: 0.6138 (Cg_exo) cc_final: 0.5935 (Cg_endo) REVERT: D 168 ILE cc_start: 0.8333 (mm) cc_final: 0.8127 (mm) REVERT: D 185 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6922 (tp30) REVERT: D 503 MET cc_start: 0.7681 (ttp) cc_final: 0.7306 (tmm) REVERT: D 538 VAL cc_start: 0.8706 (t) cc_final: 0.8493 (p) REVERT: D 585 MET cc_start: 0.9158 (mmt) cc_final: 0.8566 (mmt) REVERT: D 612 ILE cc_start: 0.8815 (mm) cc_final: 0.8588 (tp) REVERT: D 765 LYS cc_start: 0.7682 (tmmm) cc_final: 0.7470 (ttpt) REVERT: D 791 ASN cc_start: 0.8383 (m110) cc_final: 0.8151 (m110) REVERT: D 803 LEU cc_start: 0.9311 (mt) cc_final: 0.9086 (mt) outliers start: 16 outliers final: 2 residues processed: 859 average time/residue: 0.1849 time to fit residues: 247.8484 Evaluate side-chains 488 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 486 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 HIS A1152 HIS A1202 HIS B 46 HIS B 274 HIS C 93 HIS C 159 GLN C 246 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 HIS C1202 HIS D 46 HIS D 274 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132672 restraints weight = 50358.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133296 restraints weight = 78678.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135007 restraints weight = 66421.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137088 restraints weight = 41255.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137652 restraints weight = 33078.928| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28462 Z= 0.127 Angle : 0.597 11.550 38486 Z= 0.320 Chirality : 0.042 0.303 4274 Planarity : 0.005 0.081 4850 Dihedral : 6.958 88.168 3854 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -2.24 (0.12), residues: 3504 helix: -1.03 (0.11), residues: 1680 sheet: -2.28 (0.22), residues: 430 loop : -1.59 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 300 TYR 0.015 0.001 TYR C 533 PHE 0.026 0.002 PHE B 133 TRP 0.031 0.002 TRP B 158 HIS 0.005 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00272 (28452) covalent geometry : angle 0.59434 (38466) SS BOND : bond 0.00657 ( 10) SS BOND : angle 2.53875 ( 20) hydrogen bonds : bond 0.04345 ( 1199) hydrogen bonds : angle 4.64631 ( 3525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 665 time to evaluate : 1.017 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 43 LEU cc_start: 0.8379 (mt) cc_final: 0.8046 (mt) REVERT: A 79 LYS cc_start: 0.9099 (tptt) cc_final: 0.8780 (tppt) REVERT: A 95 SER cc_start: 0.8849 (m) cc_final: 0.8358 (p) REVERT: A 132 LYS cc_start: 0.8223 (tptp) cc_final: 0.8020 (tppt) REVERT: A 140 ASP cc_start: 0.7743 (m-30) cc_final: 0.7179 (t0) REVERT: A 435 HIS cc_start: 0.6543 (t-90) cc_final: 0.6216 (t-90) REVERT: A 463 MET cc_start: 0.7979 (ttp) cc_final: 0.7426 (ttp) REVERT: A 1088 LEU cc_start: 0.6976 (pp) cc_final: 0.6515 (mt) REVERT: A 1178 MET cc_start: 0.7857 (ttp) cc_final: 0.7095 (tmm) REVERT: A 1187 VAL cc_start: 0.8944 (m) cc_final: 0.8726 (m) REVERT: B 42 ARG cc_start: 0.6310 (ptm160) cc_final: 0.5670 (mtt90) REVERT: B 46 HIS cc_start: 0.6147 (OUTLIER) cc_final: 0.5914 (t-170) REVERT: B 185 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7141 (tp30) REVERT: B 197 GLU cc_start: 0.7527 (tp30) cc_final: 0.7199 (pm20) REVERT: B 363 LEU cc_start: 0.8338 (tp) cc_final: 0.8022 (tt) REVERT: B 585 MET cc_start: 0.9024 (mmt) cc_final: 0.8231 (mmt) REVERT: B 619 ASN cc_start: 0.8701 (t0) cc_final: 0.8284 (t0) REVERT: C 78 ASP cc_start: 0.7469 (t0) cc_final: 0.6427 (t0) REVERT: C 111 ILE cc_start: 0.8675 (mm) cc_final: 0.8460 (mm) REVERT: C 140 ASP cc_start: 0.7526 (m-30) cc_final: 0.6819 (t0) REVERT: C 195 ASP cc_start: 0.8026 (t70) cc_final: 0.7641 (t0) REVERT: C 262 TRP cc_start: 0.8505 (t-100) cc_final: 0.8203 (t-100) REVERT: C 304 ILE cc_start: 0.7973 (mt) cc_final: 0.7606 (mt) REVERT: C 373 TYR cc_start: 0.7690 (p90) cc_final: 0.7303 (p90) REVERT: C 463 MET cc_start: 0.7953 (ttp) cc_final: 0.7460 (ttp) REVERT: C 533 TYR cc_start: 0.7997 (t80) cc_final: 0.7698 (t80) REVERT: C 607 PHE cc_start: 0.8603 (t80) cc_final: 0.8271 (t80) REVERT: C 610 LEU cc_start: 0.9314 (tt) cc_final: 0.8962 (tp) REVERT: C 700 TYR cc_start: 0.6859 (t80) cc_final: 0.5631 (t80) REVERT: C 1088 LEU cc_start: 0.5516 (mm) cc_final: 0.4380 (pt) REVERT: C 1178 MET cc_start: 0.7941 (ttp) cc_final: 0.7341 (ttp) REVERT: C 1186 GLN cc_start: 0.7780 (tt0) cc_final: 0.7425 (tt0) REVERT: D 42 ARG cc_start: 0.6126 (ptm160) cc_final: 0.5696 (mtt90) REVERT: D 46 HIS cc_start: 0.6152 (OUTLIER) cc_final: 0.5922 (t70) REVERT: D 85 ILE cc_start: 0.8498 (mm) cc_final: 0.8281 (mm) REVERT: D 197 GLU cc_start: 0.7745 (tp30) cc_final: 0.7357 (pm20) REVERT: D 228 THR cc_start: 0.8358 (p) cc_final: 0.8108 (t) REVERT: D 330 GLU cc_start: 0.7830 (pp20) cc_final: 0.7498 (pp20) REVERT: D 363 LEU cc_start: 0.8239 (tp) cc_final: 0.7983 (tt) REVERT: D 585 MET cc_start: 0.9087 (mmt) cc_final: 0.8156 (mmt) REVERT: D 619 ASN cc_start: 0.8698 (t0) cc_final: 0.8423 (t0) REVERT: D 711 TYR cc_start: 0.7118 (t80) cc_final: 0.6800 (t80) REVERT: D 791 ASN cc_start: 0.8640 (m110) cc_final: 0.8422 (m110) REVERT: D 803 LEU cc_start: 0.9216 (mt) cc_final: 0.9005 (mt) outliers start: 2 outliers final: 0 residues processed: 667 average time/residue: 0.1604 time to fit residues: 175.9783 Evaluate side-chains 460 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 458 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 54 optimal weight: 10.0000 chunk 289 optimal weight: 0.4980 chunk 287 optimal weight: 0.0970 chunk 350 optimal weight: 0.0970 chunk 288 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 304 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 619 ASN ** A1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1181 HIS D 24 GLN D 107 HIS ** D 587 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 = 0.4021 r_free = 0.4021 target = 0.158829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133454 restraints weight = 51053.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132798 restraints weight = 77816.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134359 restraints weight = 68733.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136410 restraints weight = 43275.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136790 restraints weight = 35310.074| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28462 Z= 0.115 Angle : 0.547 7.631 38486 Z= 0.288 Chirality : 0.041 0.211 4274 Planarity : 0.004 0.065 4850 Dihedral : 6.234 79.048 3854 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3504 helix: 0.29 (0.12), residues: 1664 sheet: -2.17 (0.22), residues: 442 loop : -1.31 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 300 TYR 0.018 0.001 TYR D 673 PHE 0.029 0.001 PHE A1143 TRP 0.021 0.001 TRP B 158 HIS 0.006 0.001 HIS C1181 Details of bonding type rmsd covalent geometry : bond 0.00252 (28452) covalent geometry : angle 0.54598 (38466) SS BOND : bond 0.00286 ( 10) SS BOND : angle 1.60385 ( 20) hydrogen bonds : bond 0.03581 ( 1199) hydrogen bonds : angle 4.08872 ( 3525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 1.047 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 78 ASP cc_start: 0.7698 (t0) cc_final: 0.6525 (t0) REVERT: A 95 SER cc_start: 0.8888 (m) cc_final: 0.8530 (p) REVERT: A 140 ASP cc_start: 0.7731 (m-30) cc_final: 0.7319 (t70) REVERT: A 195 ASP cc_start: 0.8052 (t70) cc_final: 0.7770 (t0) REVERT: A 365 THR cc_start: 0.7287 (m) cc_final: 0.7065 (p) REVERT: A 427 ASP cc_start: 0.8014 (t0) cc_final: 0.7737 (t70) REVERT: A 463 MET cc_start: 0.7977 (ttp) cc_final: 0.7381 (ttp) REVERT: A 607 PHE cc_start: 0.8456 (t80) cc_final: 0.7989 (t80) REVERT: A 700 TYR cc_start: 0.6855 (t80) cc_final: 0.5624 (t80) REVERT: A 766 TRP cc_start: 0.6138 (t-100) cc_final: 0.5679 (t-100) REVERT: A 1124 VAL cc_start: 0.7712 (t) cc_final: 0.7488 (t) REVERT: A 1178 MET cc_start: 0.7730 (ttp) cc_final: 0.7235 (ttp) REVERT: A 1187 VAL cc_start: 0.8870 (m) cc_final: 0.8643 (m) REVERT: B 42 ARG cc_start: 0.6251 (ptm160) cc_final: 0.5597 (mtt90) REVERT: B 185 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6963 (tp30) REVERT: B 197 GLU cc_start: 0.7647 (tp30) cc_final: 0.7438 (pm20) REVERT: B 225 LEU cc_start: 0.8884 (mt) cc_final: 0.8606 (mt) REVERT: B 407 MET cc_start: 0.6972 (mmm) cc_final: 0.6666 (mmt) REVERT: B 408 MET cc_start: 0.4588 (mmt) cc_final: 0.4363 (pmm) REVERT: B 503 MET cc_start: 0.7771 (tmm) cc_final: 0.7443 (tmm) REVERT: B 504 ILE cc_start: 0.8567 (pt) cc_final: 0.8343 (pt) REVERT: B 619 ASN cc_start: 0.8904 (t0) cc_final: 0.8128 (t0) REVERT: B 711 TYR cc_start: 0.7144 (t80) cc_final: 0.6815 (t80) REVERT: B 716 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6843 (tppt) REVERT: B 758 VAL cc_start: 0.7060 (m) cc_final: 0.6797 (t) REVERT: B 789 LEU cc_start: 0.7423 (tp) cc_final: 0.6945 (mp) REVERT: C 95 SER cc_start: 0.8925 (m) cc_final: 0.8296 (p) REVERT: C 140 ASP cc_start: 0.7471 (m-30) cc_final: 0.7083 (t0) REVERT: C 195 ASP cc_start: 0.8068 (t70) cc_final: 0.7780 (t0) REVERT: C 373 TYR cc_start: 0.7770 (p90) cc_final: 0.7493 (p90) REVERT: C 413 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6438 (tm-30) REVERT: C 427 ASP cc_start: 0.8062 (t0) cc_final: 0.7773 (t70) REVERT: C 463 MET cc_start: 0.8030 (ttp) cc_final: 0.7400 (ttp) REVERT: C 519 ASP cc_start: 0.8367 (m-30) cc_final: 0.8045 (m-30) REVERT: C 607 PHE cc_start: 0.8564 (t80) cc_final: 0.8269 (t80) REVERT: C 610 LEU cc_start: 0.9219 (tt) cc_final: 0.8827 (tp) REVERT: C 700 TYR cc_start: 0.6701 (t80) cc_final: 0.5573 (t80) REVERT: C 1088 LEU cc_start: 0.5583 (mm) cc_final: 0.4521 (pt) REVERT: C 1178 MET cc_start: 0.8032 (ttp) cc_final: 0.6958 (ttp) REVERT: C 1186 GLN cc_start: 0.7812 (tt0) cc_final: 0.7554 (tt0) REVERT: D 42 ARG cc_start: 0.6102 (ptm160) cc_final: 0.5662 (mtt90) REVERT: D 85 ILE cc_start: 0.8580 (mm) cc_final: 0.8376 (mm) REVERT: D 185 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7200 (tp30) REVERT: D 197 GLU cc_start: 0.7761 (tp30) cc_final: 0.7540 (pm20) REVERT: D 228 THR cc_start: 0.8591 (p) cc_final: 0.8106 (t) REVERT: D 330 GLU cc_start: 0.7778 (pp20) cc_final: 0.7496 (pp20) REVERT: D 407 MET cc_start: 0.6958 (mmm) cc_final: 0.6651 (mmt) REVERT: D 503 MET cc_start: 0.7789 (tmm) cc_final: 0.7489 (tmm) REVERT: D 504 ILE cc_start: 0.8486 (pt) cc_final: 0.8274 (pt) REVERT: D 585 MET cc_start: 0.9027 (mmt) cc_final: 0.8144 (mmt) REVERT: D 619 ASN cc_start: 0.8876 (t0) cc_final: 0.8217 (t0) REVERT: D 711 TYR cc_start: 0.7162 (t80) cc_final: 0.6827 (t80) REVERT: D 758 VAL cc_start: 0.7100 (m) cc_final: 0.6851 (t) REVERT: D 791 ASN cc_start: 0.8687 (m110) cc_final: 0.8431 (m110) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.1628 time to fit residues: 163.0458 Evaluate side-chains 445 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 130 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 292 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 575 ASN A 619 ASN B 46 HIS B 83 ASN B 107 HIS B 619 ASN C 412 HIS C 575 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 107 HIS D 298 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.155944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129935 restraints weight = 51395.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130087 restraints weight = 86087.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131675 restraints weight = 70942.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133756 restraints weight = 44760.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134241 restraints weight = 35822.920| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28462 Z= 0.143 Angle : 0.566 9.625 38486 Z= 0.298 Chirality : 0.042 0.208 4274 Planarity : 0.004 0.067 4850 Dihedral : 5.792 89.288 3854 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.13 % Allowed : 2.36 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3504 helix: 0.83 (0.13), residues: 1668 sheet: -2.20 (0.23), residues: 428 loop : -1.20 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 198 TYR 0.018 0.001 TYR B 673 PHE 0.021 0.002 PHE B 133 TRP 0.030 0.002 TRP C 766 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00322 (28452) covalent geometry : angle 0.56411 (38466) SS BOND : bond 0.00502 ( 10) SS BOND : angle 2.01965 ( 20) hydrogen bonds : bond 0.03475 ( 1199) hydrogen bonds : angle 4.06809 ( 3525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 561 time to evaluate : 0.994 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 78 ASP cc_start: 0.7594 (t0) cc_final: 0.6507 (t0) REVERT: A 95 SER cc_start: 0.8934 (m) cc_final: 0.8505 (p) REVERT: A 140 ASP cc_start: 0.7729 (m-30) cc_final: 0.7198 (t70) REVERT: A 427 ASP cc_start: 0.8010 (t0) cc_final: 0.7744 (t70) REVERT: A 463 MET cc_start: 0.8054 (ttp) cc_final: 0.7430 (ttp) REVERT: A 607 PHE cc_start: 0.8639 (t80) cc_final: 0.8211 (t80) REVERT: A 766 TRP cc_start: 0.6007 (t-100) cc_final: 0.5740 (t-100) REVERT: B 42 ARG cc_start: 0.6562 (ptm160) cc_final: 0.5705 (mtt90) REVERT: B 51 GLU cc_start: 0.7502 (tt0) cc_final: 0.7060 (mp0) REVERT: B 85 ILE cc_start: 0.8595 (mm) cc_final: 0.8320 (mm) REVERT: B 185 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7002 (tp30) REVERT: B 197 GLU cc_start: 0.7693 (tp30) cc_final: 0.7313 (pm20) REVERT: B 225 LEU cc_start: 0.8922 (mt) cc_final: 0.8690 (mt) REVERT: B 407 MET cc_start: 0.6928 (mmm) cc_final: 0.6723 (mmt) REVERT: B 503 MET cc_start: 0.7701 (tmm) cc_final: 0.7194 (tmm) REVERT: B 504 ILE cc_start: 0.8625 (pt) cc_final: 0.8345 (pt) REVERT: B 518 LEU cc_start: 0.8950 (pp) cc_final: 0.8744 (pp) REVERT: B 585 MET cc_start: 0.9077 (mmt) cc_final: 0.8389 (mmt) REVERT: B 619 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8497 (t0) REVERT: C 78 ASP cc_start: 0.7415 (t0) cc_final: 0.6452 (t0) REVERT: C 95 SER cc_start: 0.8837 (m) cc_final: 0.8239 (p) REVERT: C 140 ASP cc_start: 0.7327 (m-30) cc_final: 0.6888 (t0) REVERT: C 412 HIS cc_start: 0.7440 (p90) cc_final: 0.7110 (p-80) REVERT: C 427 ASP cc_start: 0.8141 (t0) cc_final: 0.7848 (t70) REVERT: C 435 HIS cc_start: 0.6898 (t-90) cc_final: 0.6500 (t-90) REVERT: C 463 MET cc_start: 0.8094 (ttp) cc_final: 0.7433 (ttp) REVERT: C 519 ASP cc_start: 0.8393 (m-30) cc_final: 0.8100 (m-30) REVERT: C 607 PHE cc_start: 0.8686 (t80) cc_final: 0.8366 (t80) REVERT: C 610 LEU cc_start: 0.9237 (tt) cc_final: 0.8917 (tp) REVERT: C 1088 LEU cc_start: 0.5553 (mm) cc_final: 0.5284 (mt) REVERT: D 42 ARG cc_start: 0.6346 (ptm160) cc_final: 0.5722 (mtt90) REVERT: D 131 ASP cc_start: 0.7556 (p0) cc_final: 0.7246 (p0) REVERT: D 185 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7251 (tp30) REVERT: D 228 THR cc_start: 0.8744 (p) cc_final: 0.8197 (t) REVERT: D 330 GLU cc_start: 0.7810 (pp20) cc_final: 0.7510 (pp20) REVERT: D 407 MET cc_start: 0.7026 (mmm) cc_final: 0.6818 (mmt) REVERT: D 503 MET cc_start: 0.7477 (tmm) cc_final: 0.7224 (tmm) REVERT: D 585 MET cc_start: 0.9114 (mmt) cc_final: 0.8180 (mmt) REVERT: D 619 ASN cc_start: 0.8779 (t0) cc_final: 0.8306 (t0) outliers start: 4 outliers final: 0 residues processed: 564 average time/residue: 0.1633 time to fit residues: 152.3052 Evaluate side-chains 430 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 318 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 286 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 359 ASN A 412 HIS A 575 ASN A 619 ASN B 107 HIS B 587 GLN B 619 ASN C 246 GLN C 575 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.157881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131950 restraints weight = 51755.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132101 restraints weight = 74845.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133945 restraints weight = 68773.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134438 restraints weight = 43948.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135815 restraints weight = 38619.103| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28462 Z= 0.111 Angle : 0.524 8.351 38486 Z= 0.273 Chirality : 0.041 0.215 4274 Planarity : 0.004 0.062 4850 Dihedral : 5.061 75.870 3854 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3504 helix: 1.18 (0.13), residues: 1668 sheet: -2.11 (0.23), residues: 426 loop : -1.10 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 694 TYR 0.018 0.001 TYR B 673 PHE 0.018 0.001 PHE D 133 TRP 0.030 0.001 TRP C 766 HIS 0.008 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00249 (28452) covalent geometry : angle 0.52297 (38466) SS BOND : bond 0.00338 ( 10) SS BOND : angle 1.31479 ( 20) hydrogen bonds : bond 0.03118 ( 1199) hydrogen bonds : angle 3.86187 ( 3525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 0.962 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: A 78 ASP cc_start: 0.7602 (t0) cc_final: 0.6702 (t0) REVERT: A 95 SER cc_start: 0.8869 (m) cc_final: 0.8518 (p) REVERT: A 140 ASP cc_start: 0.7622 (m-30) cc_final: 0.7178 (t70) REVERT: A 427 ASP cc_start: 0.8056 (t0) cc_final: 0.7745 (t70) REVERT: A 463 MET cc_start: 0.8059 (ttp) cc_final: 0.7422 (ttp) REVERT: A 607 PHE cc_start: 0.8587 (t80) cc_final: 0.7845 (t80) REVERT: A 671 TRP cc_start: 0.9153 (t-100) cc_final: 0.8552 (t-100) REVERT: A 763 LYS cc_start: 0.7561 (tttt) cc_final: 0.7259 (tttm) REVERT: B 51 GLU cc_start: 0.7481 (tt0) cc_final: 0.7037 (mp0) REVERT: B 185 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7047 (tp30) REVERT: B 197 GLU cc_start: 0.7709 (tp30) cc_final: 0.7327 (pm20) REVERT: B 225 LEU cc_start: 0.8896 (mt) cc_final: 0.8671 (mt) REVERT: B 407 MET cc_start: 0.7143 (mmm) cc_final: 0.6819 (mmt) REVERT: B 503 MET cc_start: 0.7619 (tmm) cc_final: 0.7241 (tmm) REVERT: B 504 ILE cc_start: 0.8613 (pt) cc_final: 0.8327 (pt) REVERT: B 518 LEU cc_start: 0.8898 (pp) cc_final: 0.8681 (pp) REVERT: B 585 MET cc_start: 0.8984 (mmt) cc_final: 0.8479 (mmt) REVERT: B 619 ASN cc_start: 0.8481 (t160) cc_final: 0.8180 (t0) REVERT: B 789 LEU cc_start: 0.7333 (tp) cc_final: 0.7008 (mp) REVERT: B 803 LEU cc_start: 0.9186 (mt) cc_final: 0.8935 (mt) REVERT: C 78 ASP cc_start: 0.7576 (t0) cc_final: 0.6687 (t0) REVERT: C 95 SER cc_start: 0.8809 (m) cc_final: 0.8217 (p) REVERT: C 140 ASP cc_start: 0.7455 (m-30) cc_final: 0.6870 (t0) REVERT: C 285 THR cc_start: 0.8963 (m) cc_final: 0.8749 (m) REVERT: C 330 GLU cc_start: 0.7652 (pt0) cc_final: 0.7430 (pt0) REVERT: C 412 HIS cc_start: 0.7282 (p90) cc_final: 0.6997 (p-80) REVERT: C 427 ASP cc_start: 0.8167 (t0) cc_final: 0.7943 (t70) REVERT: C 435 HIS cc_start: 0.6863 (t-90) cc_final: 0.6517 (t-90) REVERT: C 463 MET cc_start: 0.8056 (ttp) cc_final: 0.7496 (ttp) REVERT: C 506 LYS cc_start: 0.7705 (tptt) cc_final: 0.6859 (tppt) REVERT: C 519 ASP cc_start: 0.8353 (m-30) cc_final: 0.8052 (m-30) REVERT: C 607 PHE cc_start: 0.8675 (t80) cc_final: 0.8364 (t80) REVERT: C 643 THR cc_start: 0.8671 (p) cc_final: 0.8296 (t) REVERT: C 1088 LEU cc_start: 0.5648 (mm) cc_final: 0.4638 (pt) REVERT: D 42 ARG cc_start: 0.6486 (ptm160) cc_final: 0.5732 (mtt90) REVERT: D 51 GLU cc_start: 0.7387 (tt0) cc_final: 0.6939 (mp0) REVERT: D 131 ASP cc_start: 0.7498 (p0) cc_final: 0.7175 (p0) REVERT: D 185 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7184 (tp30) REVERT: D 228 THR cc_start: 0.8732 (p) cc_final: 0.8242 (t) REVERT: D 330 GLU cc_start: 0.7775 (pp20) cc_final: 0.7528 (pp20) REVERT: D 380 MET cc_start: 0.7443 (mmm) cc_final: 0.6999 (mmm) REVERT: D 407 MET cc_start: 0.7002 (mmm) cc_final: 0.6800 (mmt) REVERT: D 518 LEU cc_start: 0.8990 (pp) cc_final: 0.8775 (pp) REVERT: D 585 MET cc_start: 0.9055 (mmt) cc_final: 0.8127 (mmt) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.1563 time to fit residues: 145.2013 Evaluate side-chains 428 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 149 optimal weight: 0.9980 chunk 310 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 287 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 575 ASN A 619 ASN A1034 GLN B 46 HIS B 107 HIS B 619 ASN C 575 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132448 restraints weight = 52239.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132060 restraints weight = 86498.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133748 restraints weight = 72517.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135338 restraints weight = 45629.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136051 restraints weight = 38645.280| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28462 Z= 0.116 Angle : 0.535 12.052 38486 Z= 0.278 Chirality : 0.041 0.234 4274 Planarity : 0.003 0.062 4850 Dihedral : 4.769 64.850 3854 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.07 % Allowed : 1.46 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3504 helix: 1.40 (0.13), residues: 1664 sheet: -1.95 (0.23), residues: 454 loop : -1.05 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 694 TYR 0.021 0.001 TYR C 702 PHE 0.021 0.001 PHE C1022 TRP 0.048 0.002 TRP D 158 HIS 0.002 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00261 (28452) covalent geometry : angle 0.53290 (38466) SS BOND : bond 0.00333 ( 10) SS BOND : angle 2.29987 ( 20) hydrogen bonds : bond 0.03114 ( 1199) hydrogen bonds : angle 3.84247 ( 3525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 552 time to evaluate : 1.153 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: A 78 ASP cc_start: 0.7573 (t0) cc_final: 0.6693 (t0) REVERT: A 95 SER cc_start: 0.8798 (m) cc_final: 0.8227 (p) REVERT: A 140 ASP cc_start: 0.7457 (m-30) cc_final: 0.7113 (t70) REVERT: A 427 ASP cc_start: 0.7926 (t0) cc_final: 0.7642 (t70) REVERT: A 463 MET cc_start: 0.8026 (ttp) cc_final: 0.7441 (ttp) REVERT: A 607 PHE cc_start: 0.8612 (t80) cc_final: 0.8051 (t80) REVERT: A 643 THR cc_start: 0.8660 (p) cc_final: 0.8183 (t) REVERT: A 671 TRP cc_start: 0.9142 (t-100) cc_final: 0.8385 (t-100) REVERT: A 732 TYR cc_start: 0.6438 (m-10) cc_final: 0.5714 (m-80) REVERT: A 763 LYS cc_start: 0.7554 (tttt) cc_final: 0.7167 (tttm) REVERT: B 51 GLU cc_start: 0.7472 (tt0) cc_final: 0.7158 (mp0) REVERT: B 85 ILE cc_start: 0.8657 (mm) cc_final: 0.8451 (mm) REVERT: B 185 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6973 (tp30) REVERT: B 518 LEU cc_start: 0.8942 (pp) cc_final: 0.8711 (pp) REVERT: B 585 MET cc_start: 0.8964 (mmt) cc_final: 0.8362 (mmt) REVERT: B 619 ASN cc_start: 0.8418 (t160) cc_final: 0.7881 (t0) REVERT: B 720 THR cc_start: 0.8201 (p) cc_final: 0.7910 (p) REVERT: B 789 LEU cc_start: 0.7349 (tp) cc_final: 0.7064 (mp) REVERT: C 78 ASP cc_start: 0.7627 (t0) cc_final: 0.6767 (t0) REVERT: C 95 SER cc_start: 0.8802 (m) cc_final: 0.8196 (p) REVERT: C 140 ASP cc_start: 0.7407 (m-30) cc_final: 0.6913 (t0) REVERT: C 330 GLU cc_start: 0.7607 (pt0) cc_final: 0.7319 (pt0) REVERT: C 412 HIS cc_start: 0.7346 (p90) cc_final: 0.6905 (p-80) REVERT: C 427 ASP cc_start: 0.8086 (t0) cc_final: 0.7803 (t70) REVERT: C 435 HIS cc_start: 0.6758 (t-90) cc_final: 0.6451 (t-90) REVERT: C 463 MET cc_start: 0.8101 (ttp) cc_final: 0.7486 (ttp) REVERT: C 519 ASP cc_start: 0.8438 (m-30) cc_final: 0.8032 (m-30) REVERT: C 533 TYR cc_start: 0.7866 (t80) cc_final: 0.7366 (t80) REVERT: C 587 GLN cc_start: 0.8129 (mm110) cc_final: 0.7914 (mm110) REVERT: C 607 PHE cc_start: 0.8644 (t80) cc_final: 0.8319 (t80) REVERT: C 643 THR cc_start: 0.8624 (p) cc_final: 0.8285 (t) REVERT: C 1088 LEU cc_start: 0.5566 (mm) cc_final: 0.4588 (pt) REVERT: D 42 ARG cc_start: 0.6558 (ptm160) cc_final: 0.5764 (mtt90) REVERT: D 85 ILE cc_start: 0.8648 (mm) cc_final: 0.8437 (mm) REVERT: D 131 ASP cc_start: 0.7398 (p0) cc_final: 0.6956 (p0) REVERT: D 132 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7849 (mttp) REVERT: D 185 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7229 (tp30) REVERT: D 228 THR cc_start: 0.8771 (p) cc_final: 0.8216 (t) REVERT: D 330 GLU cc_start: 0.7775 (pp20) cc_final: 0.7530 (pp20) REVERT: D 380 MET cc_start: 0.7523 (mmm) cc_final: 0.6994 (mmm) REVERT: D 503 MET cc_start: 0.7552 (tmm) cc_final: 0.7339 (tmm) REVERT: D 518 LEU cc_start: 0.9066 (pp) cc_final: 0.8818 (pp) REVERT: D 585 MET cc_start: 0.9095 (mmt) cc_final: 0.8037 (mmt) REVERT: D 816 TYR cc_start: 0.6284 (m-80) cc_final: 0.6075 (m-80) outliers start: 2 outliers final: 0 residues processed: 554 average time/residue: 0.1570 time to fit residues: 146.7895 Evaluate side-chains 432 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 301 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 302 optimal weight: 0.6980 chunk 331 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 107 HIS B 619 ASN C 575 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.158818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131895 restraints weight = 52321.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132572 restraints weight = 77587.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134755 restraints weight = 68534.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134920 restraints weight = 45411.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136190 restraints weight = 39247.215| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28462 Z= 0.108 Angle : 0.530 10.358 38486 Z= 0.273 Chirality : 0.041 0.222 4274 Planarity : 0.004 0.071 4850 Dihedral : 4.628 59.979 3854 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3504 helix: 1.53 (0.13), residues: 1676 sheet: -1.95 (0.23), residues: 450 loop : -0.98 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 694 TYR 0.021 0.001 TYR C 702 PHE 0.024 0.001 PHE C1210 TRP 0.032 0.001 TRP B 158 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00242 (28452) covalent geometry : angle 0.52827 (38466) SS BOND : bond 0.00343 ( 10) SS BOND : angle 1.83657 ( 20) hydrogen bonds : bond 0.02995 ( 1199) hydrogen bonds : angle 3.77857 ( 3525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.986 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: A 78 ASP cc_start: 0.7645 (t0) cc_final: 0.6820 (t0) REVERT: A 132 LYS cc_start: 0.8071 (tptp) cc_final: 0.7835 (tppt) REVERT: A 140 ASP cc_start: 0.7444 (m-30) cc_final: 0.7122 (t70) REVERT: A 190 ARG cc_start: 0.8194 (mmm160) cc_final: 0.7952 (mmm160) REVERT: A 427 ASP cc_start: 0.8043 (t0) cc_final: 0.7724 (t70) REVERT: A 463 MET cc_start: 0.8107 (ttp) cc_final: 0.7504 (ttp) REVERT: A 533 TYR cc_start: 0.8080 (t80) cc_final: 0.7865 (t80) REVERT: A 643 THR cc_start: 0.8639 (p) cc_final: 0.8257 (t) REVERT: A 671 TRP cc_start: 0.9110 (t-100) cc_final: 0.8893 (t-100) REVERT: A 732 TYR cc_start: 0.6336 (m-10) cc_final: 0.5900 (m-80) REVERT: A 763 LYS cc_start: 0.7547 (tttt) cc_final: 0.7126 (tttm) REVERT: B 51 GLU cc_start: 0.7495 (tt0) cc_final: 0.7118 (mp0) REVERT: B 112 GLN cc_start: 0.7759 (mt0) cc_final: 0.7495 (mt0) REVERT: B 185 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6961 (tp30) REVERT: B 518 LEU cc_start: 0.8973 (pp) cc_final: 0.8722 (pp) REVERT: B 585 MET cc_start: 0.8965 (mmt) cc_final: 0.8373 (mmt) REVERT: B 619 ASN cc_start: 0.8535 (t160) cc_final: 0.7896 (t0) REVERT: B 789 LEU cc_start: 0.7449 (tp) cc_final: 0.7185 (mp) REVERT: C 33 MET cc_start: 0.6947 (mmm) cc_final: 0.6724 (mmt) REVERT: C 65 GLN cc_start: 0.8429 (mp10) cc_final: 0.7864 (mp10) REVERT: C 78 ASP cc_start: 0.7706 (t0) cc_final: 0.6959 (t0) REVERT: C 95 SER cc_start: 0.8864 (m) cc_final: 0.8228 (p) REVERT: C 140 ASP cc_start: 0.7407 (m-30) cc_final: 0.7072 (t70) REVERT: C 330 GLU cc_start: 0.7600 (pt0) cc_final: 0.7332 (pt0) REVERT: C 412 HIS cc_start: 0.7286 (p90) cc_final: 0.6876 (p-80) REVERT: C 427 ASP cc_start: 0.8110 (t0) cc_final: 0.7860 (t70) REVERT: C 463 MET cc_start: 0.8108 (ttp) cc_final: 0.7488 (ttp) REVERT: C 519 ASP cc_start: 0.8279 (m-30) cc_final: 0.8015 (m-30) REVERT: C 643 THR cc_start: 0.8640 (p) cc_final: 0.8306 (t) REVERT: C 671 TRP cc_start: 0.9057 (t-100) cc_final: 0.7915 (t-100) REVERT: C 1088 LEU cc_start: 0.5501 (mm) cc_final: 0.4613 (pt) REVERT: D 131 ASP cc_start: 0.7376 (p0) cc_final: 0.6955 (p0) REVERT: D 132 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7806 (mttp) REVERT: D 185 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7261 (tp30) REVERT: D 228 THR cc_start: 0.8756 (p) cc_final: 0.8300 (t) REVERT: D 330 GLU cc_start: 0.7811 (pp20) cc_final: 0.7563 (pp20) REVERT: D 585 MET cc_start: 0.9095 (mmt) cc_final: 0.8889 (mmt) REVERT: D 791 ASN cc_start: 0.8666 (m110) cc_final: 0.8395 (m110) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.1479 time to fit residues: 133.8260 Evaluate side-chains 427 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 199 optimal weight: 0.9980 chunk 345 optimal weight: 0.9980 chunk 318 optimal weight: 0.3980 chunk 311 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 185 optimal weight: 0.5980 chunk 140 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 343 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 24 GLN B 46 HIS B 107 HIS B 619 ASN C 219 HIS C 575 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133037 restraints weight = 52366.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134997 restraints weight = 78623.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136150 restraints weight = 63545.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136488 restraints weight = 46644.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138425 restraints weight = 38924.837| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28462 Z= 0.108 Angle : 0.534 12.977 38486 Z= 0.276 Chirality : 0.041 0.225 4274 Planarity : 0.004 0.060 4850 Dihedral : 4.528 57.493 3854 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.07 % Allowed : 0.63 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3504 helix: 1.64 (0.13), residues: 1674 sheet: -1.90 (0.23), residues: 446 loop : -0.92 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 694 TYR 0.021 0.001 TYR C 702 PHE 0.019 0.001 PHE C1022 TRP 0.031 0.001 TRP D 158 HIS 0.003 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00243 (28452) covalent geometry : angle 0.53163 (38466) SS BOND : bond 0.00501 ( 10) SS BOND : angle 2.26825 ( 20) hydrogen bonds : bond 0.03007 ( 1199) hydrogen bonds : angle 3.76318 ( 3525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 0.675 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: A 71 TYR cc_start: 0.7515 (m-80) cc_final: 0.7289 (m-80) REVERT: A 78 ASP cc_start: 0.7695 (t0) cc_final: 0.6857 (t0) REVERT: A 95 SER cc_start: 0.8962 (m) cc_final: 0.8288 (p) REVERT: A 132 LYS cc_start: 0.7961 (tptp) cc_final: 0.7677 (tppt) REVERT: A 140 ASP cc_start: 0.7494 (m-30) cc_final: 0.7211 (t70) REVERT: A 190 ARG cc_start: 0.8271 (mmm160) cc_final: 0.8019 (mmm160) REVERT: A 427 ASP cc_start: 0.7941 (t0) cc_final: 0.7691 (t70) REVERT: A 463 MET cc_start: 0.8125 (ttp) cc_final: 0.7545 (ttp) REVERT: A 607 PHE cc_start: 0.8532 (t80) cc_final: 0.7828 (t80) REVERT: A 643 THR cc_start: 0.8645 (p) cc_final: 0.8210 (t) REVERT: A 671 TRP cc_start: 0.9098 (t-100) cc_final: 0.8869 (t-100) REVERT: A 763 LYS cc_start: 0.7340 (tttt) cc_final: 0.7073 (tttm) REVERT: A 784 THR cc_start: 0.7699 (p) cc_final: 0.7490 (p) REVERT: B 51 GLU cc_start: 0.7464 (tt0) cc_final: 0.7067 (mp0) REVERT: B 85 ILE cc_start: 0.8628 (mm) cc_final: 0.8420 (mm) REVERT: B 112 GLN cc_start: 0.7563 (mt0) cc_final: 0.6725 (pt0) REVERT: B 126 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 185 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6942 (tp30) REVERT: B 503 MET cc_start: 0.7827 (tmm) cc_final: 0.7605 (tmm) REVERT: B 518 LEU cc_start: 0.8962 (pp) cc_final: 0.8692 (pp) REVERT: B 585 MET cc_start: 0.8949 (mmt) cc_final: 0.8434 (mmt) REVERT: B 619 ASN cc_start: 0.8620 (t160) cc_final: 0.8080 (t0) REVERT: C 65 GLN cc_start: 0.8413 (mp10) cc_final: 0.7912 (mp10) REVERT: C 78 ASP cc_start: 0.7687 (t0) cc_final: 0.6982 (t0) REVERT: C 95 SER cc_start: 0.8799 (m) cc_final: 0.8134 (p) REVERT: C 140 ASP cc_start: 0.7291 (m-30) cc_final: 0.7066 (t70) REVERT: C 330 GLU cc_start: 0.7605 (pt0) cc_final: 0.7329 (pt0) REVERT: C 412 HIS cc_start: 0.7197 (p90) cc_final: 0.6796 (p-80) REVERT: C 427 ASP cc_start: 0.7984 (t0) cc_final: 0.7748 (t70) REVERT: C 463 MET cc_start: 0.8099 (ttp) cc_final: 0.7494 (ttp) REVERT: C 519 ASP cc_start: 0.8262 (m-30) cc_final: 0.8016 (m-30) REVERT: C 533 TYR cc_start: 0.7915 (t80) cc_final: 0.7541 (t80) REVERT: C 643 THR cc_start: 0.8631 (p) cc_final: 0.8270 (t) REVERT: C 671 TRP cc_start: 0.9036 (t-100) cc_final: 0.7940 (t-100) REVERT: C 1088 LEU cc_start: 0.5474 (mm) cc_final: 0.4619 (pt) REVERT: D 112 GLN cc_start: 0.7878 (mt0) cc_final: 0.7118 (pt0) REVERT: D 126 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7287 (mm-30) REVERT: D 131 ASP cc_start: 0.7380 (p0) cc_final: 0.6928 (p0) REVERT: D 132 LYS cc_start: 0.8244 (mmtp) cc_final: 0.7678 (mttp) REVERT: D 185 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7234 (tp30) REVERT: D 228 THR cc_start: 0.8828 (p) cc_final: 0.8330 (t) REVERT: D 330 GLU cc_start: 0.7904 (pp20) cc_final: 0.7481 (pp20) REVERT: D 585 MET cc_start: 0.9088 (mmt) cc_final: 0.8430 (mmt) REVERT: D 791 ASN cc_start: 0.8643 (m110) cc_final: 0.8436 (m110) outliers start: 2 outliers final: 0 residues processed: 550 average time/residue: 0.1450 time to fit residues: 135.0517 Evaluate side-chains 439 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 333 optimal weight: 0.2980 chunk 171 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 110 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 107 HIS B 619 ASN C 575 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 107 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.159994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134255 restraints weight = 52636.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135267 restraints weight = 85878.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136928 restraints weight = 67388.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138368 restraints weight = 43085.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138835 restraints weight = 37659.640| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28462 Z= 0.102 Angle : 0.538 9.553 38486 Z= 0.274 Chirality : 0.041 0.213 4274 Planarity : 0.003 0.051 4850 Dihedral : 4.389 55.312 3854 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3504 helix: 1.71 (0.13), residues: 1674 sheet: -1.88 (0.24), residues: 444 loop : -0.90 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 694 TYR 0.023 0.001 TYR C 702 PHE 0.018 0.001 PHE C1022 TRP 0.028 0.001 TRP D 158 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00229 (28452) covalent geometry : angle 0.53559 (38466) SS BOND : bond 0.00446 ( 10) SS BOND : angle 2.19188 ( 20) hydrogen bonds : bond 0.02899 ( 1199) hydrogen bonds : angle 3.72069 ( 3525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 1.054 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: A 71 TYR cc_start: 0.7530 (m-80) cc_final: 0.7277 (m-80) REVERT: A 78 ASP cc_start: 0.7722 (t0) cc_final: 0.6906 (t0) REVERT: A 95 SER cc_start: 0.8923 (m) cc_final: 0.8229 (p) REVERT: A 132 LYS cc_start: 0.7891 (tptp) cc_final: 0.7608 (tppt) REVERT: A 140 ASP cc_start: 0.7541 (m-30) cc_final: 0.7316 (t70) REVERT: A 190 ARG cc_start: 0.8319 (mmm160) cc_final: 0.8113 (mmm160) REVERT: A 195 ASP cc_start: 0.8146 (t0) cc_final: 0.7932 (p0) REVERT: A 427 ASP cc_start: 0.7961 (t0) cc_final: 0.7726 (t70) REVERT: A 463 MET cc_start: 0.8082 (ttp) cc_final: 0.7097 (ttp) REVERT: A 607 PHE cc_start: 0.8521 (t80) cc_final: 0.7790 (t80) REVERT: A 643 THR cc_start: 0.8638 (p) cc_final: 0.8226 (t) REVERT: A 671 TRP cc_start: 0.9084 (t-100) cc_final: 0.8850 (t-100) REVERT: A 1178 MET cc_start: 0.7566 (ttp) cc_final: 0.7268 (tmm) REVERT: B 51 GLU cc_start: 0.7437 (tt0) cc_final: 0.7069 (mp0) REVERT: B 112 GLN cc_start: 0.7614 (mt0) cc_final: 0.6689 (pt0) REVERT: B 126 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7361 (mm-30) REVERT: B 185 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6910 (tp30) REVERT: B 228 THR cc_start: 0.8776 (p) cc_final: 0.8262 (t) REVERT: B 585 MET cc_start: 0.8870 (mmt) cc_final: 0.8401 (mmt) REVERT: B 619 ASN cc_start: 0.8524 (t160) cc_final: 0.7994 (t0) REVERT: B 789 LEU cc_start: 0.7423 (tp) cc_final: 0.7070 (mp) REVERT: C 33 MET cc_start: 0.6887 (mmm) cc_final: 0.6625 (mmt) REVERT: C 78 ASP cc_start: 0.7721 (t0) cc_final: 0.6990 (t0) REVERT: C 95 SER cc_start: 0.8801 (m) cc_final: 0.8129 (p) REVERT: C 330 GLU cc_start: 0.7618 (pt0) cc_final: 0.7323 (pt0) REVERT: C 412 HIS cc_start: 0.7287 (p90) cc_final: 0.6913 (p-80) REVERT: C 427 ASP cc_start: 0.7961 (t0) cc_final: 0.7758 (t70) REVERT: C 463 MET cc_start: 0.8094 (ttp) cc_final: 0.7521 (ttp) REVERT: C 489 ILE cc_start: 0.8950 (pt) cc_final: 0.8686 (mm) REVERT: C 533 TYR cc_start: 0.7925 (t80) cc_final: 0.7446 (t80) REVERT: C 643 THR cc_start: 0.8623 (p) cc_final: 0.8231 (t) REVERT: C 671 TRP cc_start: 0.9071 (t-100) cc_final: 0.7974 (t-100) REVERT: C 1088 LEU cc_start: 0.5497 (mm) cc_final: 0.4670 (pt) REVERT: D 112 GLN cc_start: 0.7858 (mt0) cc_final: 0.6921 (pt0) REVERT: D 126 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7331 (mm-30) REVERT: D 131 ASP cc_start: 0.7304 (p0) cc_final: 0.6867 (p0) REVERT: D 132 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7633 (mttp) REVERT: D 185 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7203 (tp30) REVERT: D 228 THR cc_start: 0.8777 (p) cc_final: 0.8355 (t) REVERT: D 289 VAL cc_start: 0.7866 (t) cc_final: 0.7639 (t) REVERT: D 330 GLU cc_start: 0.7931 (pp20) cc_final: 0.7527 (pp20) REVERT: D 585 MET cc_start: 0.9081 (mmt) cc_final: 0.8413 (mmt) REVERT: D 619 ASN cc_start: 0.8428 (t160) cc_final: 0.8119 (t0) REVERT: D 708 MET cc_start: 0.6553 (ptp) cc_final: 0.6272 (ptp) REVERT: D 791 ASN cc_start: 0.8591 (m110) cc_final: 0.8385 (m110) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.1511 time to fit residues: 142.5095 Evaluate side-chains 433 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 340 optimal weight: 0.5980 chunk 289 optimal weight: 0.1980 chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 619 ASN A1034 GLN B 46 HIS B 83 ASN B 107 HIS B 619 ASN C 575 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 83 ASN D 107 HIS D 112 GLN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133463 restraints weight = 52489.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134107 restraints weight = 77936.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135472 restraints weight = 67395.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137616 restraints weight = 41636.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138020 restraints weight = 32878.747| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28462 Z= 0.109 Angle : 0.547 9.604 38486 Z= 0.281 Chirality : 0.041 0.212 4274 Planarity : 0.003 0.051 4850 Dihedral : 4.419 53.905 3854 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3504 helix: 1.76 (0.13), residues: 1666 sheet: -1.82 (0.23), residues: 454 loop : -0.90 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 694 TYR 0.019 0.001 TYR A 702 PHE 0.029 0.001 PHE C1210 TRP 0.028 0.002 TRP D 158 HIS 0.003 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00247 (28452) covalent geometry : angle 0.54534 (38466) SS BOND : bond 0.00355 ( 10) SS BOND : angle 2.04725 ( 20) hydrogen bonds : bond 0.02960 ( 1199) hydrogen bonds : angle 3.75089 ( 3525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 541 time to evaluate : 0.895 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 71 TYR cc_start: 0.7581 (m-80) cc_final: 0.7342 (m-80) REVERT: A 78 ASP cc_start: 0.7692 (t0) cc_final: 0.6917 (t0) REVERT: A 95 SER cc_start: 0.8990 (m) cc_final: 0.8325 (p) REVERT: A 132 LYS cc_start: 0.7846 (tptp) cc_final: 0.7547 (tppt) REVERT: A 140 ASP cc_start: 0.7623 (m-30) cc_final: 0.7258 (t70) REVERT: A 190 ARG cc_start: 0.8404 (mmm160) cc_final: 0.8163 (mmm160) REVERT: A 195 ASP cc_start: 0.8128 (t0) cc_final: 0.7913 (p0) REVERT: A 427 ASP cc_start: 0.7974 (t0) cc_final: 0.7699 (t70) REVERT: A 463 MET cc_start: 0.8117 (ttp) cc_final: 0.7562 (ttp) REVERT: A 607 PHE cc_start: 0.8601 (t80) cc_final: 0.8002 (t80) REVERT: A 643 THR cc_start: 0.8703 (p) cc_final: 0.8272 (t) REVERT: A 671 TRP cc_start: 0.9103 (t-100) cc_final: 0.8869 (t-100) REVERT: B 51 GLU cc_start: 0.7445 (tt0) cc_final: 0.7026 (mp0) REVERT: B 85 ILE cc_start: 0.8667 (mm) cc_final: 0.8452 (mm) REVERT: B 112 GLN cc_start: 0.7622 (mt0) cc_final: 0.6750 (pt0) REVERT: B 126 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 185 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6925 (tp30) REVERT: B 228 THR cc_start: 0.8864 (p) cc_final: 0.8354 (t) REVERT: B 585 MET cc_start: 0.8919 (mmt) cc_final: 0.8442 (mmt) REVERT: B 619 ASN cc_start: 0.8520 (t160) cc_final: 0.8081 (t0) REVERT: B 708 MET cc_start: 0.6643 (ptp) cc_final: 0.6439 (ptp) REVERT: C 33 MET cc_start: 0.7007 (mmm) cc_final: 0.6786 (mmt) REVERT: C 95 SER cc_start: 0.8796 (m) cc_final: 0.8190 (p) REVERT: C 412 HIS cc_start: 0.7458 (p90) cc_final: 0.6989 (p-80) REVERT: C 427 ASP cc_start: 0.8066 (t0) cc_final: 0.7862 (t70) REVERT: C 463 MET cc_start: 0.8138 (ttp) cc_final: 0.7120 (ttp) REVERT: C 489 ILE cc_start: 0.8975 (pt) cc_final: 0.8711 (mm) REVERT: C 527 MET cc_start: 0.6754 (mmm) cc_final: 0.6518 (tpp) REVERT: C 533 TYR cc_start: 0.7950 (t80) cc_final: 0.7468 (t80) REVERT: C 643 THR cc_start: 0.8713 (p) cc_final: 0.8318 (t) REVERT: C 1088 LEU cc_start: 0.5569 (mm) cc_final: 0.4668 (pt) REVERT: C 1176 LEU cc_start: 0.8567 (tp) cc_final: 0.8360 (tp) REVERT: C 1178 MET cc_start: 0.7490 (tmm) cc_final: 0.7169 (ttp) REVERT: D 112 GLN cc_start: 0.7890 (mt0) cc_final: 0.6828 (pt0) REVERT: D 126 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7352 (mm-30) REVERT: D 131 ASP cc_start: 0.7272 (p0) cc_final: 0.6863 (p0) REVERT: D 132 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7659 (mttp) REVERT: D 185 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7168 (tp30) REVERT: D 228 THR cc_start: 0.8829 (p) cc_final: 0.8416 (t) REVERT: D 289 VAL cc_start: 0.7868 (t) cc_final: 0.7665 (t) REVERT: D 330 GLU cc_start: 0.7922 (pp20) cc_final: 0.7564 (pp20) REVERT: D 585 MET cc_start: 0.9074 (mmt) cc_final: 0.8348 (mmt) REVERT: D 708 MET cc_start: 0.6628 (ptp) cc_final: 0.6312 (ptp) REVERT: D 711 TYR cc_start: 0.7130 (t80) cc_final: 0.6692 (t80) REVERT: D 791 ASN cc_start: 0.8665 (m110) cc_final: 0.8365 (m110) outliers start: 3 outliers final: 0 residues processed: 543 average time/residue: 0.1523 time to fit residues: 139.7941 Evaluate side-chains 431 residues out of total 3006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 344 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 318 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 118 optimal weight: 0.0570 chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 412 HIS A 575 ASN A 587 GLN A 619 ASN B 107 HIS B 619 ASN C 575 ASN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132637 restraints weight = 52344.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133550 restraints weight = 77435.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134924 restraints weight = 65987.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136672 restraints weight = 42271.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137196 restraints weight = 34735.015| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28462 Z= 0.117 Angle : 0.560 9.567 38486 Z= 0.287 Chirality : 0.041 0.213 4274 Planarity : 0.003 0.051 4850 Dihedral : 4.468 51.685 3854 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3504 helix: 1.72 (0.13), residues: 1672 sheet: -1.88 (0.23), residues: 454 loop : -0.89 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 694 TYR 0.016 0.001 TYR A 702 PHE 0.028 0.001 PHE C1210 TRP 0.029 0.002 TRP D 158 HIS 0.008 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00267 (28452) covalent geometry : angle 0.55787 (38466) SS BOND : bond 0.00360 ( 10) SS BOND : angle 2.02450 ( 20) hydrogen bonds : bond 0.03057 ( 1199) hydrogen bonds : angle 3.81411 ( 3525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.13 seconds wall clock time: 78 minutes 20.45 seconds (4700.45 seconds total)